MODEL SELECTION REPORT 
University of Louisiana at Lafayette 
Ehab A. Meselhe, PhD, PE 
Alonso Griborio, PhD 
Jeanne Arceneaux, EI 
Report #LOXA05-001 
FINAL 
June 2006 

TABLE OF CONTENTS 
1. INTRODUCTION................................................................................................... 5
1.1. Background ................................................................................................... 5
1.2. Landscape: Refuge Vegetation, Soils and Physiography ................................ 7
1.3. Hydrology and Hydrodynamic Description................................................... 8
1.3.1. Precipitation......................................................................................... 8
1.3.1.1. Spatial Distribution of Rainfall in the Loxahatchee Refuge............. 11
1.3.2. Evapotranspiration ............................................................................ 12
1.3.3. Water Levels..................................................................................... 13
1.3.4. Hydroperiods and Water Depths ....................................................... 15
1.3.5. Discharge.......................................................................................... 17
1.3.6. Groundwater ..................................................................................... 19
1.3.7. Hydrologic Budget of the Refuge...................................................... 21
1.3.8. Refuge Water Management – Regulation Schedule ........................... 21
1.3.9. Hydrodynamics................................................................................. 23
1.4. Water Quality.............................................................................................. 27
2. LITERATURE REVIEW ..................................................................................... 29
2.1. Historical Review of Previous Modeling Effort for the Refuge .................... 29
2.2. Previous Modeling Effort in other Wetland Systems.................................... 35
3. OBJECTIVES AND NEED FOR RESEARCH................................................... 41
3.1. Project Description. ..................................................................................... 42
3.1.1. Phase I: Preparation of Data……………………………………........ 42
3.1.2. Phase II: Model Implementation………………………………… ...... 43
4. MODEL SELECTION.......................................................................................... 46
4.1. Candidate Models ........................................................................................ 46
4.2. Model Evaluation Sheet............................................................................... 46
4.3. Model Selection Criteria .............................................................................. 49
4.4. Preliminary Evaluation Results.................................................................... 50
4.5. Resource Models ......................................................................................... 55
5. SUMMARY ........................................................................................................... 56
6. CITED REFERENCES ........................................................................................ 57
7. CONSULTED REFERENCES............................................................................. 64
8. APPENDIX A: CANDIDATE MODELS- EVALUATION SHEETS 
9. APPENDIX B: RESOURCE MODELS- EVALUATION SHEETS 
LIST OF FIGURES
Figure 1. Historic and Current Flow Conditions for the Everglades System 5
Figure 2. Map of Water Conservation Areas (WCAs)..................................................... 6
Figure 3. Location of Rain Gages and Weather Stations ................................................ 9
Figure 4. Seasonal Variation of Rainfall in the Loxahatchee Refuge............................ 10
Figure 5. Annual Variation of Rainfall ........................................................................ 10
Figure 6. Spatial Distribution of Annual Average Rainfall in the Loxahatchee Refuge 11
Figure 7. Seasonal Variation of ET Estimated at STA-1W .......................................... 13
Figure 8. Water Level Monitoring Stations in the Loxahatchee Refuge ...................... 14
Figure 9. Average Marsh Water Level in the Loxahatchee Refuge .............................. 14
Figure 10. Bathymetric Contours for the Loxahatchee Refuge...................................... 15
Figure 11. Water Depths in the Loxahatchee Refuge for Different Water Levels .......... 16
Figure 12. Location of Hydraulic Structures in the Loxahatchee Refuge...................... 19
Figure 13. Water Regulation Schedule for Water Conservation Area 1......................... 23
Figure 14. Thalweg Profiles for the Sediment Surface Elevation and Channel Bottom Elevation 
For the Western Canals (L-7 and L-39)....................................................... 24
Figure 15. Thalweg Profiles for the Sediment Surface Elevation and Channel Bottom Elevation 
For the Eastern Canals (L-40) ..................................................................... 25

LIST OF TABLES 
Table 1. Cumulative Inflows and Outflows to the Loxahatchee Refuge ....................... 18
Table 2. Overland Flow Coefficients ........................................................................... 26
Table 3. Summary of Project Deliverables……………………………………............. 45
Table 4. Model Selection Matrix ................................................................................ 51
Table 5. Additional Pros and Cons of Selected Models… 54

1. INTRODUCTION 
1.1. Background 
The Arthur R. Marshall Loxahatchee National Wildlife Refuge (hereafter referred to as the 
Loxahatchee Refuge or simply as the Refuge) is the only remnant of the northern Everglades in 
Palm Beach County, Florida (USFWS, 2000). It includes 143,238 acres (58,000 ha) and is 
located seven miles west of the city of Boynton Beach. Being part of the Everglades, it is part of 
a much larger watershed, i.e., the Kissimmee-Okeechobee-Everglades system. Historically, the 
Kissimmee River discharged into Lake Okeechobee, and during wet cycles the lake would 
overflow its south bank, providing additional flow to the Everglades (Light and Dineen, 1994). 
According to Raghunathan et al. (2001) this water would sheet flow across the Everglades, but 
now, water flows through canals and structures, and through a series of water storage areas 
(Water Conservation Areas, WCA), to the Everglades National Park (ENP). In the nineteen 
forties, the U.S. Army Corps of Engineer (USACOE) constructed three impoundment areas 
(WCA1, 2 and 3), bounded by levees and connected by a series of canals. In 1951, the 
Loxahatchee Refuge was established at Water Conservation Area 1 (USFWS, 2000). Figure 1 
shows the historic and the current flow condition for the Kissimmee-Okeechobee-Everglades 
system. 
Loxahatchee Refuge 
Figure 1. Historic and Current Flow Patterns for the Everglades System. 
[Adapted from the Comprehensive Everglades Restoration Plan website, http://www.evergladesplan.org/index.cfm]

As indicated by Richardson et al. (1990), the Refuge is now isolated from the historic 
Kissimmee-Okeechobee-Everglades watershed as it is completely enclosed within a levee system 
and a borrow canal along the interior of the levee. As shown in Figure 2, the Refuge is bordered 
on the northwest by drained agricultural land, the Everglades Agricultural Area (EAA), and by 
mainly an urban development at the east. Water Conservation Area 2A is located at the 
southwest of the Refuge. 
Figure 2. Map of Water Conservation Areas (WCAs) 
[Adapted from the Reef Relief Website, http://www.reefrelief.org/Floridabay/report_page4.html]
From a historic perspective regarding water control in the Everglades, Light and Dineen (1994) 
indicated that the WCAs were designed to accomplish eight objectives: 1) receive and store 
agricultural runoff from the EAA, 2) prevent water accumulated in the system from overflowing 
into urban and agricultural areas, 3) recharge regional aquifers, 4) prevent salt water intrusion, 5) 
store and convey water supply for agricultural, municipal and industrial use, and for the ENP 
requirements, 6) receive controlled releases from Lake Okeechobee, 7) protect wildlife and 
promote recreation, and 8) dampen the effect of hurricane-induced wind tides by maintaining 

marsh vegetation in the system. The Comprehensive Conservation Plan developed by the U.S. 
Fish and Wildlife Service (USFWS, 2000) emphasizes the role of the Refuge in the South 
Florida Ecosystem and its use for the national migratory bird management program. The USFWS 
indicated that in consistency with the South Florida Ecosystem Plan, the Refuge should be used 
to accomplish the following: 1) reduce exotic species, 2) manage water quality and quantity 
through partnerships, 3) monitor and inventory wildlife and habitats, 4) promote public 
awareness about the ecosystem, and 5) provide wildlife-compatible recreation. 
1.2. Landscape: Refuge Vegetation, Soils and Physiography 
The Refuge landscape consist of a complex mosaic of wetland communities that grade from 
wetter areas such as sloughs and wet prairies, to sawgrass, brush, and finally tree islands 
occurring at the dryer end of the scale. Sloughs are the deepest natural marsh communities in the 
Everglades with water depth that may exceed 3 feet in the wet season; the annually average 
depth is about 1 foot (USFWS, 2000). Sloughs are typically found in the south part of the 
Refuge. In contrast to sloughs, wet prairies have shallow water levels. They are prevalent 
vegetative community in the Refuge with approximately 50 % land coverage. Wet prairies are 
the primary community type on the central portion of the Refuge (Richardson et al., 1990). 
Sawgrass accounts for about 25% of land coverage. It is present on all part of the Refuge 
including a vast area on the west side. The tree islands cover approximately 20% of the Refuge 
interior. They are basically located at the northern portion of the Refuge ranging in size from less 
than 1 acre to more than 300 acres (USFWS, 2000). In addition to the aforementioned species, 
Cattails also grows on the Refuge. The cattail has developed in the Refuge as a response to the 
anthropogenic load of nutrients in the incoming water. According to Richardson et al. (1990) 
almost all of the cattail is found within the first 1000 meters of the canal and literally the 
remaining cattail is found within the next 1000 meters. Cattail is more abundant in the west side 
of the Refuge. 
The Refuge wetland communities occur on top of a bed of peat (Richardson et al., 1990) from 
seven to nine feet deep (Scheidt et al. 2000; Stober et al. 1996). The peat is lightly colored, 
fibrous and spongy, reflective of high organic content (USFWS, 2000; Stober et al. 1996). It is 
important to notice that the Refuge is located in a depression in the underlying-limestone-

bedrock Fort Thompson Formation, which results in greater water depth than the surrounding 
Everglades. However, in contrast to other areas of the Everglades where there are only shallow 
layers of soils, soil depth in the Refuge range from 3.6 to 14.0 feet (Silveira, 1996). 
Regional topographic surveys by the United State Geological Survey (USGS) provide elevation 
data to parameterize hydrologic and ecologic numerical simulation models that are being 
developed for ecosystem restoration activities. It should be noted that modeling of sheet flow and 
water surface levels in the wetlands of South Florida is very sensitive to changes in elevation due 
to the expansive and extremely low relief terrain. Therefore, vertical accuracy on the order of +/15 
centimeters is required for the elevation data for use as input to hydrologic models (Desmond, 
2003). 
1.3. Hydrologicand Hydrodynamic Description 
This section describes the major characteristics of the Refuge’s hydrology and hydrodynamics. 
These descriptions are based on published information and information processed by the authors 
for the Period of Record (POR) that goes from January 1, 1995 to December 31, 2004. This 
period was selected for calibration and validation of the model to be developed (Meselhe et al., 
2005) and will be referred in this report as the POR. 
1.3.1. Precipitation 
According to Abtew et al. (2005) South Florida is a high-rainfall region, with frontal, convective 
and tropical system-driven rainfall events. They indicated that the annual average rainfall on the 
entire region managed by the SFWMD is 52.8 inches (this value was obtained from varying 
lengths or record for each station and from a varying number of stations, in general the periods of 
record went from 1900 to 2000), being the annual average for WCA-1 slightly lower than this 
value. Rainfall is the only important type of precipitation in the Refuge. 
Using precipitation data from stations S-5A, S-6, S-39, STA1W, WCA1ME, LOXWS, PS-1 
(Gage 8), PS-2 (Gage 10), and South Shore South End Gage (Gage 6); and using multiple 
Thiessen polygons it was found that the annual average rainfall for the Loxahatchee Refuge is 

about 52.1 inches, for the POR from 1995 to 2004. Multiple Thiessen polygons were used to 
account for the missing data, i.e, for each day in which data was missing for one or more 
stations, the areas of the polygons were altered so that the stations with missing data were not 
included. Similarly, it was found that the maximum daily and monthly values for the POR are 
about 6.5 and 18.1 inches, respectively. Figure 3 shows the location of the rain gages. The reader 
is referred to Meselhe et al. (2005) for information about the data acquisition and processing. 
Figure 3. Location of Rain Gages and Weather Stations 
In terms of the seasonal variability, Meselhe et al. (2005) reported that more rainfall occurs 
during the months of June to October, compared to the rest of the year. In fact, the “wet season” 
for South Florida runs from June through October and accounts for 66% of the annual rainfall 
(Sklar et al., 2002). A monthly rainfall analysis for the studied POR (1995 – 2004) indicates that 
June is the wettest months with about 7.7 inches, followed by September with 7.5 inches. On the 
other hand, the driest month are January and December with 1.8 and 1.9 inches, respectively. 
The seasonal rainfall variation for the studied POR is shown in Figure 4. 

9
8
Monthly Rainfall (inches)
7
6
5
4
3
2
1
0
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec 
Figure 4. Seasonal Variation of Rainfall in the Loxahatchee Refuge 
An annual (calendar year) analysis of rainfall data for the POR, shows a steady distribution for 
the first five year (1994 to 1999) with an annual value of about 58 inches per year, a sever 
drought in 2000 (annual average equal to 38.9 inches) and 1999 as the wettest year with 59.1 
inches per year. From 2002 to 2004 the annual rainfall dropped below 50 inches with an average 
value of about 46 inches per year. Figure 5 shows the annual variation of rainfall for Refuge. 
0 
10 
20 
30 
40 
50 
60 
70Annual Rainfall (inches) 
1994 1996 1998 2000 2002 2004 2006 
Figure 5. Annual Variation of Rainfall 

1.3.1.1. Spatial Distribution of Rainfall in the Loxahatchee Refuge. 
Figure 6 shows the spatial distribution of annual average rainfall in the Loxahatchee Refuge, 
estimated for the period of time between January 1, 1997 and December 31, 2004. This figure is 
based on the information of 8 active rain gages during the aforementioned period. This period 
was selected because gages 8 and 10 started operating in January 1, 1997. As can be observed in 
this figure, the northeastern part of the Refuge received more rainfall compared to the other 
areas. Conversely, the west and southwest received the least amount of rain. The difference 
between the zones with the highest and the least amount of rainfall is notorious. This difference 
is about 19 inches of rain per year. Is important to notice that the research team conducted a 
thorough evaluation of the rain gages’ data, and did not find reasons to avoid the use of any 
particular gage. 
S-6 
WCA1ME 
LOXWS 
S-5A 
STA1W 
(ENRP) 
Gage 8 
Gage 10 
S-39 
Figure 6. Spatial Distribution of Annual Average Rainfall in the Loxahatchee Refuge 

1.3.2. Evapotranspiration 
According to Abtew et al. (2005) rainfall and evapotranspiration (ET) are the main parameters in 
the hydrologic balance of the Everglades. They indicate that the balance between rainfall and ET 
maintains the hydrology system in either a wet or dry condition. They also indicate that, in South 
Florida, most of the variation in ET is explained by solar radiation. Sklar et al. (2003) and 
Abtew et al. (2004) reported that the estimated ET for WCA-1 for water years 2003 and 2004 is 
about 51.1 inches. 
Evapotranspiration data for the Loxahatchee Refuge are available from one station located at the 
Everglades Nutrients Removal Project (ENRP) (See Figure 3) currently the Stormwater 
Treatment Area 1-W (STA-1W). For the POR, the annual average measured ET from STA-1W 
station is equal to 52.1 inches. This station is always wet so the measured ET might be higher 
than the actual ET in the Refuge. Griborio et al. (2006) estimated the actual ET for the Refuge 
using the observed ET from STA-1W (ETobs) using the following equation: 
ET = fET ETobs (1)
H
where fET = f Maximum ET min, Minimum,1( ))
( 
H 
ET
fETmin is the minimum reduction of ET because of shallow depth = 20%.
H is the marsh water depth so that H = Maximum,0 ( E -E0).
M 
E0 is the marsh ground elevation
HET is the depth below which ET is reduced = 0.25 m.
Using Eq. 1 and the data from station STA-1W, Griborio et al. (2006) found the annual average 
ET for the Refuge is about 47.2 inches per year. Figure 7 shows the ET’s seasonal variation 
estimated from STA-1W for the POR. As can be observed in this figure, ET is higher during the 
months of March to August (with values higher than 4.5 inches), reaching a peak of about 6 
inches in May. A regional evaluation of ET in the everglades conducted by German (2000) 
presented similar results to those shown in Figure 7. 

0 
1 
2 
3 
4 
5 
6 
7 
Monthly Evapotranspiration (inches) 
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec 
Figure 7. Seasonal Variation of ET Estimated at STA-1W (adapted from Meselhe et al., 2005) 
1.3.3. Water Levels 
The water levels in the Refuge change due to Precipitation, ET, seepage, and surface water 
management. According to Abtew et al. (2005) the historic daily average stage (for the period 
1960 to 2004) for the Refuge is 15.56 ft NGVD. They indicated that water level was compiled 
from four sites: 1-8C, 1-7, 1-8T, and 1-9. The location of these gages is shown in Figure 8. For 
the POR, Meselhe et al. (2005) found that the arithmetic mean of daily average marsh water 
levels for the Refuge is 16.45 ft NGVD29. For this period, a maximum daily average marsh 
water level of 18.19 ft NGVD29 occurred on October 16, 1999 (during Hurricane Irene); and a 
minimum marsh water level of 14.94 ft NGVD29 was attained on May 21, 2001. Meselhe et al. 
(2005) compiled and evaluated data from five gages located in the marsh, i.e., North, 1-7, 1-8T, 
1-9 and South, and one gage locate in the rim canal, i.e, gage 1-8C (See Figure 8). For gage 18C, 
the arithmetic mean of daily average water levels is 16.31 ft NGVD29 (for the POR), and 
the maximum and minimum daily average stages are 18.19 and 12.06 ft NGVD29, respectively. 
The minimum daily water level for the canal was reached on May 23, 2002. Figure 9 shows the 
average marsh water level in the Refuge for the studied POR. More information about the water 
level data for the Refuge is presented in the Report by Meselhe et al. (2005). 

Water Level (ft NGVD) 
Figure 8. Water Level Monitoring Stations in the Loxahatchee Refuge (adapted from Meselhe et 
al., 2005) 
19.0 
18.5 
18.0 
17.5 
17.0 
16.5 
16.0 
15.5 
15.0 
14.5 
14.0 
Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 
Figure 9. Average Marsh Water Level in the Loxahatchee Refuge. 

1.3.4. Hydroperiod and Water Depths 
Elevation data for the Refuge are available from the USGS on a 400 by 400 meter grid with 
horizontal and vertical accuracy of +/- 15 cm. (Desmond, 2003). Based on these data, the 
bathymetric contours for the Refuge (excluding the rim channel) range from 18.50 to 10.61 ft 
NGVD29, with a mean elevation of about 15.00 ft NGVD29. Figure 10 shows the bathymetric 
contours for the Loxahatchee Refuge based on the USGS’s data. Based on the average water 
level (16.45 ft NGVD29) and the mean elevation for the Refuge, we obtain an average depth of 
about 1.45 ft (for the POR). Assuming a flat pool at the average water level and taking into 
account the refuge bathymetry, the maximum and minimum depths would be equal to 5.84 ft and 
0 ft, respectively. Figure 11 shows the distribution of water depths in the Refuge for different 
stages (assuming a flat pool). In this figure it can be observed that the spatial distribution of 
water depth roughly corresponds to the inverse of topography with the northern part of the 
Refuge being shallower than the southern. 
Figure 10. Bathymetric Contours for the Loxahatchee Refuge (ft NGVD29 
In terms of hydroperiod the north and south regions of the Refuge are very distinct (as can be 
observed in Figure 11). The north end has a much greater variance in hydroperiod than the south 

end. During low water levels, the north part of the Refuge is much more susceptible to staying 
dry for long periods; while in the south, the dry season is not as likely to completely dewater the 
marsh for months at a time (Richardson et al., 1990). 
Richardson et al. (1990) presented a hydrologic evaluation of the Refuge over a 16 year period 
(1970 – 1986). They found that the 16-year hydroperiod over the entire Refuge ranges from 70% 
to 98% exhibiting an obvious north-south trend of increasing hydroperiod with localized 
anomalies corresponding to topographic features. Richardson et al. (1990) found that mean water 
depths for the entire 16 year period range from 0.2 ft in the north end to 3.2 ft in the south. The 
estimated average water level for this 16 year period is about 15.8 ft NGVD. 
Water Level = 17.00 ft NGVD Water Level = 16.45 ft NGVD 
Water Level = 16.00 ft NGVD Water Level = 15.50 ft NGVD 
Figure 11. Water Depths in the Loxahatchee Refuge for Different Water Levels 

1.3.5. Discharge 
Inflows and outflows are important components of the Refuge’s water budget. Runoff enters the 
refuge through the pump stations G-251, and G-310 (STA-1W), the Acme 1 and Acme 2 (via 
gate G-94D) pump stations, and historically received discharge from the now-diverted S-6 pump 
station (diverted to STA-2, May 10, 2001) and the S-5A (diverted to STA-1W in August 26, 
1999). At times, significant flows continue to be discharged from the S-5A through bypass gates 
G-300 and G-301 directly into the Refuge. Bypass of the S-6 discharge directly to the refuge is 
possible through bypass gate G-338, but such bypasses have not occurred since diversion. Pump 
station S-362 will soon also be discharging to the refuge from STA-1E. Figure 12 shows the 
location of these pumping stations. The S-5A station pumps water from the West Palm Beach 
Canal, the G-251 and G-310 pump water from the Stormwater Treatment Area 1-W, and the S-6 
station pumps water to the Hillsboro (L-39 canal, see Figure 12). According to USFWS (2000) 
the amount of water pumped from S-6 was about 155,000 acre-feet per year, representing nearly 
30% of the runoff that came in through structures. This water loss needs to be compensated by 
increasing flows through the G-310 station and Stormwater Treatment Area 1-E and/or by 
reduction in outflows from the Refuge. These changes in water management may have water 
quality impacts that need to be evaluated. 
The water outlet structures on the Refuge are G-94A, B, and C that provide water supply to the 
Lake Worth Drainage District (LWDD) on the east side, and the S-10 and S-39 spillways on the 
south and west side (USFWS, 2000). The S-10 consists of three spillways, i.e, S-10A, S-10C and 
S-10D (S-10B was proposed but never constructed), and functions as a flood control gate 
operated by the Corps of Engineers. The S-10E consists of three 6-foot diameter gated culverts, 
and it is operated as an additional outlet from WCA-1 (see Figure 12) by the SFWMD. The S-39 
is operated to make water supply releases from the Refuge during the dry season, and to 
discharge excess water to the ocean when capacity is available in the Hillsboro Canal and water 
is not needed in WCA-2 or -3. Water may also be released at the north end of the Refuge through 
the G-300 and G-301 to the C-51 Canal via the S-5AS for water supply. 
Meselhe et al. (2005) presented an evaluation of the Refuge hydraulic structures’ flow data for 
the period of record between January 1, 1994 and December 31, 2004. For this period, they 

found that the yearly average inflow and outflow to the Refuge (through hydraulic structures) are 
579,038 and 576,141 acre-ft, respectively. Table 1 shows the total cumulative inflows and 
outflows from hydraulic structures into and out of the Loxahatchee Refuge. 
Table 1. Cumulative Inflows and Outflows to the Loxahatchee Refuge -Flow Through Water 
Control Structures for the Period Between January 1995 and December 2004. (After Meselhe et 
al., 2005) 
Total 
Operational Dates Operative Daily Net Inflow Net outflow 
Days during Average Volume Volume 
Structure Type of Flow Type of Flow Start End the POR Flow (cfs) (Ac-ft) (Ac-ft) 
S-5A Pump Station Inflow 1/1/1995 8/26/1999 1698 391.8 1,319,556 0 
S-5AS Spillway Bidirectional 1/1/1995 6/7/1999 1618 112.8 0 362,004 
G-300 Spillway Bidirectional 8/26/1999 12/31/2004 1954 2.4 9,302 0 
G-301 Spillway Bidirectional 8/26/1999 12/27/2004 1950 28.4 109,845 0 
G-310 Pump Station Inflow 7/7/2000 12/31/2004 1638 411.0 1,335,308 0 
G-251 Pump Station Inflow 1/1/1995 12/31/2004 3652 118.6 859,095 0 
S-6 Pump Station Inflow 1/1/1995 5/15/2001 2326 398.6 1,838,963 0 
S-10E Culvert Outflow 1/1/1995 12/31/2004 3652 33.4 0 241,937 
G-338 Culvert Inflow 1/1/1995 5/15/2001 2326 0.0 0 0 
S-10D Spillway Outflow 1/1/1995 12/31/2004 3652 175.9 0 1,274,156 
S-10C Spillway Outflow 1/1/1995 12/31/2004 3652 146.3 0 1,059,744 
S-10A Spillway Outflow 1/1/1995 12/31/2004 3652 141.4 0 1,024,250 
S-39 Spillway Outflow 1/1/1995 12/31/2004 3652 184.7 0 1,337,900 
S-362 Pump Station Inflow 9/21/2004 12/31/2004 101 99.2 19,873 0 
ACME # 1 Pump Station Inflow 1/1/1995 12/31/2004 3652 21.4 155,014 0 
ACME # 2 Pump Station Inflow 1/1/1995 12/31/2004 3652 19.8 143,424 0 
G-94C Culvert Bidirectional 1/1/1995 12/31/2004 3652 38.7 0 280,329 
G-94B Culvert Outflow 1/1/1995 12/31/2004 3652 4.7 0 34,045 
G-94A Culvert Outflow 1/1/1995 12/31/2004 3652 20.3 0 147,046 
Total 5,790,380 5,761,411 

Figure 12. Location of Hydraulic Structures in the Loxahatchee Refuge (adapted from Meselhe 
et al., 2005) 
1.3.6. Groundwater 
Renken et al. (2005) indicated that Southeastern Florida is underlain by Holocene- to Tertiary-
age karstic limestone deposits that form (in descending order): a highly prolific surficial aquifer 
system, a poorly permeable intermediate confining system, and a permeable Floridian aquifer. 
The surficial aquifer system contains water under unconfined conditions with discharging 
occurring to canals, the Atlantic Ocean and ET. The surficial aquifer system serves as the 
principal source of water supply for the Palm Beach County (Renken et al., 2005). According to 
Miller (1988) the average thickness of the surficial aquifer in the Palm Beach County is about 
200 feet. Miller (1988) further divided the surficial aquifer in Palm Beach County into three 
zones: (1) Zone I, is the most permeable part of the surficial aquifer system with transmissivities 
in the range of 1,000 ft2/s to 100,000 ft2/s; (2) Zone II, is a zone in general less permeable than 
Zone I with an average transmissivity of about 5,360 ft2/s; and (3) Zone III, is the least 
permeable part of the aquifer system. For Zone III, Miller stated this zone presents “nearly 

impermeable marls which almost totally prevent infiltration of surface water in most of the area.” 
According to Miller, most of the Loxahatchee Refuge is in Zone III with just a thin band of the 
Refuge east in Zone I and a small portion of the south-east in Zone II. As indicated by Welter 
(2002), Miller findings suggest that, in the Loxahatchee Refuge, surface water processes are 
much more important than ground water processes. 
Ground-water levels are highest near the impounded WCAs and lowest near the coast; 
consequently, the hydraulic gradient in southeastern Florida is seaward and the movement of 
groundwater is east and southeast toward the coast (Renken et al., 2005). Water levels are 
highest in September to October (end of wet season) and lowest during April or May (end of dry 
season). Renken et al. (2005) showed that for the east boundary of the Refuge, the average water 
level in the surficial aquifer varied from 16 to 14 ft NGVD29, for the period 1990-1994. Miller 
(1988) showed that the elevation of the water table around the Refuge varied between 12 ft 
NGVD29 and 14 ft NGVD29, for the year 1984. 
The groundwater information inside the Refuge is very scarce. In fact, there are no groundwater 
stations in the interior of the Refuge. The general consent is that since water levels in the Refuge 
are consistently higher than surrounding levels, seepage is usually out of the Refuge (Trimble, 
1986; Lin and Gregg, 1998; Welter, 2002; Griborio et al., 2006). Several water budget and 
hydrodynamic model for the Refuge has neglected the effect of groundwater in the basis that 
groundwater processes are much less important than surface processes (Richardson et al., 1990; 
Miller, 1998; Walker, 1995; Munson et al., 2002). However, the estimations presented by Lin 
and Gregg (1998) and Griborio et al. (2006) indicate that seepage may account for about 5% to 
9% of the water outflow from the Refuge. Griborio et al. (2006) used the following equation to 
estimate the rate of loss of groundwater recharge in the canal or marsh: 
Gi = ri seep (Ei -EB ) (2) 
-
where i = m or l for levee (canal) or marsh, respectively. 
r
seep-l is the levee seepage rate constant = 6.x10-2 d-1 (Lin and Gregg, 1988). 
r
seep-m is the marsh seepage rate constant = 4.x10-6 d-1. 
EB is the boundary water surface elevation = 11.5 ft NGVD (3.5 m). 

1.3.7. Hydrologic Budget of the Refuge 
The water entering the Loxahatchee Refuge comes from two main sources rainfall and 
agricultural and urban runoff. Rainfall constitutes approximately 56 to 60 percent of the total 
input as reported by USFWS (2000) and Richardson et al. (1990). For the selected 10-year POR 
(1995-2004), the average annual inflow from hydraulic structures is about 579,038 Ac-ft and the 
average annual inflow from precipitation is about 621,836 Ac-ft. These amounts total an annual 
total inflow of 1,200,874 Ac-ft with precipitation representing the 51.8% and inflow from 
structures the 48.2%. 
Water leaves the Refuge by ET, infiltration, levee leakage, or through a series of control 
structures. For the POR, the average annual outflow from hydraulic structures is equal to 
576,141 Ac-ft. For the same period, the estimated ET and seepage are 563,160 Ac-ft and 61,570 
Ac-ft, respectively. Based on these values, outflow through structures represents the 48.0 % of 
the total outflow and ET and seepage represent 46.9% and 5.1%, respectively. 
1.3.8. Refuge Water Management -Regulation Schedule 
Following approximately five years of analysis and negotiation, the current Refuge Water 
Regulation Schedule was established in May, 1995, and it is administered by the U.S. Army 
Corps of Engineers (US Army Corps of Engineers Jacksonville District 1994). The Refuge 
Water Regulation Schedule is described in detail in the Comprehensive Conservation Plan for 
the Refuge (USFWS, 2000), and is summarized below: 
Purpose and Management: regulate the water level in WCA-1 to produce maximum benefits for 
flood control, water supply, fish and wildlife, and prevention of salt water intrusion. To meet 
these objectives, water level in the Refuge is adjusted during the year either by release or pump 
water into the refuge or by a combination of both. A schematic diagram of the water regulation 
schedule is shown in Figure 13. 
Schedule: the water regulation time schedule is grouped into four zones (Neidrauer 2004): 
• Zone A1: is the flood control zone from January through June. When water levels reach 
this zone, active water releases will be made through the S-10 spillway (and S-39 
when agreed between USACE and SFWMD). Water supply releases as needed. 

• Zone A2: from July through December, attempts are made to maintain water levels 
within this zone. In this zone, water levels in the Refuge, which are linked with 
rainfall amounts and the water level at Lake Okeechobee, are permitted to reach a 
maximum of 17.5 feet NGVD29. Excess water is released from the S-10 and S-39 
spillways. When additional water is needed for WCA-2A or other areas, it is 
released from the Refuge depending on relative water level at Lake Okeechobee. 
If Lake Okeechobee stage is above WCA-1 stage or no more than one foot below, 
then water supply releases from WCA-1 must be preceded by an equivalent 
volume of inflow (Neidrauer, 2004). 
• Zone B: is the water supply zone, and ranges from a minimum of 14.0 to 17.5 feet 
NGVD 29 during the year. When water levels in the Refuge are within this zone, 
water releases are allowed, as needed depending on the water level at Lake 
Okeechobee. If Lake Okeechobee stage is above WCA-1 stage or no more than 
one foot below, then water supply releases from WCA-1 must be preceded by an 
equivalent volume of inflow (Neidrauer, 2004). This is the zone considered to be 
most beneficial to fish and wildlife of the Refuge (USFWS, 2000). 
• Zone C: when water levels drop to 14.0 feet NGVD or less, there would be no net 
release of water from the Refuge. Any water supply releases must be preceded by 
an equivalent volume of inflow. 
Benefits of Water Regulation Schedule (USFWS, 2000): 
• Increased hydroperiod of interior marshes to avoid annual dryout. 
• Increased water depth during the wet years in the northern portion of the Refuge. 
• Increased area of interior marsh which serves as nursery areas for aquatic organisms. 
• Improvement in timing of winter stage drawdown to benefit wading birds 
• Restoration of deep water habitats suitable for nesting Everglades snail kites. 
• Greater water storage within the central and southern Florida project system during wet 
and normal rainfall years 

12 
13 
14 
15 
16 
17 
18 
Water Elevation (NGVD feet) 
ZONE A1 
ZONE B 
Water releases, as needed, depending upon elevation at Lake Okeechobee 
Active ZONE A2 
Water releases 
linked to amount of 
rainfall and elevation 
at Lake Okeechobee 
ZONE C 
No net water releases due to drought 
w ater releases, due to flood conditions 
JanuaryFebruaryMarch 
April 
MayJune 
JulyAugust
SeptemberOctoberNovemberDecember 
Figure 13. Water Regulation Schedule for Water Conservation Area 1 (Adapted from 
Comprehensive Conservation Plan for the Loxahatchee National Wildlife Refuge, USFWS, 
2000) 
There are current discussions of revising the Refuge regulation schedule to take into account 
newer data and understanding of hydrological, ecological, and water quality relationships. 
Analyses supporting management decisions concerning alternative schedule revisions should 
utilize the model being discussed in this report. 
1.3.9. Hydrodynamic 
Two major features define the hydrodynamic of the Loxahatchee Refuge: a rim canal and the 
marsh interior. Figure 12 shows the location of the canals around the Refuge. Naturally these two 
features interact among them, but in a limited manner. All of the water that is pumped into the 
Refuge goes into the canals and much of this water move through the canals around the 
perimeter and leaves the Refuge directly through the southwestern and eastern structures. 
Richardson et al. (1990) indicated that much of the water in the interior part of the Refuge comes 
from rainfall, and that the interior is basically a rainfall driven system. This conclusion is 
strongly supported by patterns of mineral constituent concentrations in the interior (Richardson 
et al. 1990; Weaver and Payne 2004). 

The Refuge rim canal can be divided in two major systems, i.e., the western system that is 
formed by the L-7 and L-39 canals and the eastern system that is formed by the L-40 canal (see 
Figure 12). For the western canals, the sediment surface elevations range between 7.0 and -1.5 ft 
Elevation (ft NGVD29) 
NGVD29 with a mean elevation equal to 2.4 ft. For the L-40 canal, the sediment surface 
elevations range between 6.7 and -5.7 ft NGVD29 with a mean elevation equal to 3.2 ft. The top 
width ranges between 205 and 120 ft for the western canal, and between 173 and 88 ft for the L40 
canal, the mean top widths are 169.7 and 121.5 ft for the western and for the L-40 canals, 
respectively. The thalweg profiles for the sediment surface elevations and for the channel bottom 
elevations are presented in Figures 14 and 15, for the L-7/L39 canals and for the L-40 canal, 
respectively. The profiles for the L-7/L-39 canals are quite irregular with almost a horizontal 
average slope. On the other hand, the profile for the L-40 canal is better defined with a north to 
south mild slope of about 3.2 inches per mile. For the POR, the average depths in the L-7/L-39 
canal systems vary between 17.9 ft and 9.4 ft, with a mean depth of about 14.1 ft. For the L-40 
canal the water depths vary between 22.0 ft and 9.8 ft with a mean depth of about 13.2 ft. 
18
16
14
12
10
8
6
4
2
0
-2
-4
-6
-8
-10 
-12 
0 5 1015202530 
L-7 Canal L-39 Canal 
Canal Mile 
Sed. Surf. Ele. 
Channel Bot. Elev. 
Figure 14. Thalweg Profiles for the Sediment Surface Elevation and Channel Bottom Elevation 
for the Western Canals (L-7 and L-39) (adapted from Meselhe et al., 2005) 

18 
16 
14 
12 
10 
8 
6 
4 
2 
0 
-2 
-4 
-6 
-8
-10
-12
0 5 1015202530 
Elevation (ft NGVD29) 
Canal Mile 
Sed. Surf. Ele. 
Channel Bot. Elev. 
Figure 15. Thalweg Profiles for the Sediment Surface Elevation and Channel Bottom Elevation 
for the Eastern Canal (L-40) (adapted from Meselhe et al., 2005) 
The marsh area of the Refuge has a very mild north to south slope, which results in a slow 
southward flow movement (Meselhe et al., 2005). The north to south slope is about 1 inch per 
mile. As indicated in a previous section, for the POR, the average water depth in the marsh area 
of the Refuge is about 1.45 ft ranging between 0 ft and 5.84 ft. 
There are not water velocity measurements in the Loxahatchee Refuge, neither in the canal nor in 
the marsh. However, the estimated velocity in the marsh is about 100 m/d (Waldon, 2005). This 
value agrees with the results of tracer experiment conducted by Saiers et al. (2003) at a wetland 
in the Florida Everglades. They found the mean surface-water velocity to be equal to 5.3 m/h 
(about 127 m/d). Saiers et al. (2003) results indicated that longitudinal, lateral and vertical 
diffusion were small, and nearly equal to 0.16, 0.15 and 0.001 m2/h, respectively. The U.S. Army 
Corp of Engineers (Ferguson, 2002) presented estimation of canal water velocities at the junction 
of the L-40 canal and the S-362 discharge canal using a 2-Dimensional (2-D) hydrodynamic 
model. The predicted velocities in the junction were 0.1, 0.2 and 0.8 feet per second for 
discharges of 550, 960 and 4200 cfs, respectively. 

The flow resistance in the marsh area is affected by vegetation and water depth. Naturally, there 
is significant increase in flow resistance due to vegetation. Similarly, the flow resistance 
increases as the water depth decreases. Shih and Rahi (1982) presented the field evaluation of 
Manning’s roughness coefficient in a Floridian slough marsh. They found that Manning’s n 
ranged from 0.16 to 0.55 as the water depth varied from 0.40 to 0.65 m. Rosendahl (1980) also 
presented a field investigation of Manning’s Roughness Coefficient and longitudinal dispersion 
coefficients in the Everglades marsh. Rosendahl found that Manning’s n varied between 0.43 and 
2.76 for water depths between 0.2 and 2.0 ft. He also found that the longitudinal dispersion 
coefficient varied between 0.37 and 22 m2/hr. In the application of the South Florida Water 
Management Model (SFWMM), MacVicar et al. (1984) calibrated the friction losses for 
overland flow. They found good results using the following relationship for Manning’s n: 
a n Hb (3)
= 
Where H is the water depth in ft, and a and b are usually equal to 0.5 and -0.77. Using Eq. 3 and 
the average depth of 1.45, the average Manning’s n for the Refuge is about 0.38. 
Barnes and Tarboton (2002) provided a list of a and b coefficients for different land uses and 
vegetative communities. These values were provided as starting values for the South Florida 
Water Management Model (SFWMM) 2000 calibration effort. Table 2 shows an overview of 
these coefficients. 
Table 2. Overland Flow Coefficients for Eq. 1 (after Barnes and Tarboton, 2002) 
Manning's n Coefficients Manning's n Coefficients 
Land Use Type a b Land Use Type a b 
Urban .080 - 0.200 0.00 Cattail 1.110 -0.77 
Citrus 0.2250 0.00 Mix Cattail/Sawgrass 1.110 -0.77 
Row Crops 0.2250 0.00 Wet Prairie 1.200 -0.77 
Sugar Cane 0.2250 0.00 STA 1.350 -0.77 
Irrigated Pasture 0.2250 0.00 Forested Wetland 0.155 -0.77 
Shrubland 1.5500 -0.77 Forested Uplands 0.850 0.00 
Marl Prairie 0.6000 -0.77 Mangroves 0.950 -0.77 
Ridge & Slough 0.700 - 1.000 -0.77 Melaleuca 0.350 -0.77 
Sawgrass Plains 1.1100 -0.77 Water 0.010 0.00 
Barnes and Tarboton (2002) specified that Ridge and Slough are the predominant vegetation 
cover for WCA-1 with an “a ” coefficient equal to 0.9 and a “b” coefficient equal to -0.77. 

There is not concrete information about the effect of wind in the Refuge’s hydrodynamic. 
However, since the density of emergent vegetation in the Refuge is very high, is it not expected 
that wind will be a major forcing component. Even though, the effect of wind will be included in 
the modeling effort. 
1.4. Water Quality 
Along with the changes in water quantity and timing, changes in water quality are introducing 
negative impacts to the Everglades ecosystem (Richardson et al., 1990; Walker, 1991 and 1995; 
Davis et al., 1994; Light and Dineen, 1994; McCormick et al., 1996; USFWS, 2000; Brandtl et 
al., 2000; Raghunathan et al., 2001; Childers et al., 2003). The Everglades ecosystem is 
characteristically oligotrophic (Childers et al., 2003) and phosphorus limited (McCormick et al., 
1996, Raghunathan et al., 2001) and is comprised of species that have evolved to develop under 
low nutrient conditions (USFWS, 2000). According to Childers et al. (2003) water column total 
phosphorus concentrations in the Everglades are typically less than 10 mg/L. It is well 
documented that water flowing into the Everglades has an important load of nutrients and other 
contaminants (e.g., Richardson et al., 1990, Stober et al., 1996; USFWS, 2000). Nutrient loading 
from urban areas and the EAA has significantly increased nutrient concentrations, particularly 
phosphorus, in the water conservation areas (USFWS, 2000). Childers et al. (2003) reported that 
in northern Everglades regions, near the EAA, total phosphorus concentrations often exceed 100 
mg/L. Atmospheric deposition is another important source of nutrients. Richardson et al. (1990) 
reported that, from 1979 through 1988, atmospheric deposition accounted for 25% of the P and 
15% of the N entering the Refuge compared to 75% of the P and 84% of the N entering via S5 
and S6 combined. 
Despite the specific values reported by Richardson et al. (1990), the estimate of average rainfall 
phosphorus concentration is uncertain, and analysis of aerial deposition data is statistically 
challenging (Ahn 1999a; Ahn 1999b; Ahn and James 1999a; Ahn and James 1999b; Grimshaw 
and Dolske 2002; Pollman et al. 2002; Redfield 2002; Walker and Jewell 1997). Measurements 
of atmospheric deposition rates are complicated by numerous sources of contamination which 
can cause positive bias. Estimates of atmospheric phosphorus deposition have ranged from 17 to 
96 mg/m2 per year for different locations in South Florida (Walker, 1995). Most modeling 

approaches for the Everglades have used a constant value for the atmospheric phosphorus 
deposition. Walker (1995) assumed a constant value of 43 mg/m2-yr for an area adjacent to the 
Refuge. Raghunathan et al. (2001) used a temporally and spatially constant value of 43 mg/m2-
yr. Munson et al. (2002) used an equivalent rainfall concentration of 30 ppb (about 35 mg/m2-
yr). It will be particularly challenging to correctly address atmospheric deposition in this 
modeling effort. 
The Refuge is unique in that most of the high nutrient water received from the control structures 
remains in the rim canals without actually flowing through the interior of the Refuge. Some high 
nutrient water does move into the Refuge, but evidence indicates that it moves slowly and affects 
only a limited distance of habitat near the canals (USFWS, 2000). Richardson et al. (1990) 
indicated that there is a large central core area of water in the interior of the Refuge whose 
nutrient composition is typical of rain water atmospheric deposition, surrounded by an area with 
a higher nutrient composition affected by the pumped inflows to the perimeter canal. USFWS 
(2000) reported that areas in the western, southwestern, southern, and southeastern portions of 
the Refuge are currently being eutrophied by nutrients inputs. 
Wetlands respond to nutrient enrichment with characteristic increases in soil nutrients and shifts 
in plant community compositions (Childers et al. 2003). Among the negative effects from 
increased nutrients are: loss of native sawgrass communities, conversion of wet prairie plant 
communities to cattails, invasion of exotic plants, and loss of important habitats for wading birds 
(USFWS, 2000). Important efforts are being made to reduce the nutrient load entering the 
Everglades ecosystem, e.g., construction of Stormwater Treatment Areas. However, Childers et 
al. (2003) found that, even though water quality improved throughout much of the Everglades in 
the 1990s, water quality impacts worsened during such time in areas of the northern Everglades. 
For the Loxahatchee Refuge, Childers et al. (2003) found that zones of high phosphorus 
(exceeding 700 mg P/Kg dry wt. soil) increased to more that 1 Km from the western margin 
canal, between the period from 1989 and 1999. For the same period they found that cattail-
dominated marsh increased from 0.5 to 1.0 Km, measured east from the S-6 pump station. It is 
important to notice that there is some level of uncertainty in Childers et al. (2003) results for the 
Loxahatchee Refuge, since he reported a transect length of 30 Km (west to east across the 

Refuge from the S-6 pump structure to the L-40 boundary canal), while such a transect is only 22 
Km. 
2. LITERATURE REVIEW 
2.1. Historical Review of Previous Modeling Effort for the Refuge 
Significant efforts have been devoted to model the hydrology and water quality of the 
Loxahatchee Refuge, alone or as a part of the greater Everglades. This section provides a 
chronological review of documented-past modeling efforts related to the Refuge: 
• Lin (1979) adapted and modified the Receiving Water Quantity Model (EPA, 1971) to model 
the Water Conservation Areas in order to investigate the hydraulic impact of additional 
inflow under different pumping scenarios. Lin (1979) modeled Water Conservation Areas 1, 
2A and 3A with 20 link-nodes each. The network system for WCA1 contained 20 nodes and 
57 channels. The calibration of the model was based on comparison of predicted and 
observed stages at selected gages. The model was calibrated for the 1974 year data, and then 
was applied to the period from 1962 to 1973. For WCA1, predicted and recorded values at 
gages S-6, 1-8, 1-7 and 1-9 were compared. It should be noted that gages S-6 and 1-8 are 
located in the existing canal system, while 1-7 and 1-9 are located in the central marshland of 
the Refuge. For the validation period, important deviations were observed between the 
model results and the measurements. The deviation for interior gages was far less than the 
one in the canal system. Lin (1979) recommended that the number of nodes in the network 
system should be increased in order to provide a better representation of the real water body, 
and also that some existing relationship in the model should be improved (see Lin, 1979, for 
details). The investigator did not model groundwater or water quality in the study. 
• MacVicar et al. (1984) presented the application of the South Florida Water Management 
Model (SFWMM) to two planning areas, the Lower East Coast (LEC) and the Upper East 
Coast (UEC). The WCA1 was included in the LEC model that also included the other Water 
Conservation Areas, the Everglades Agricultural Area, most of Big Cypress National 
Preserve, Everglades National Park, and the urban areas of the LEC that covered Dade, 
Broward, Palm Beach, and parts of Monroe and Collier Counties. A two by two mile node 

spacing was used to cover the 6,880 square miles area modeled. A time step of one day was 
used. The model was able to simulate overland, channel and groundwater flow. McVicar et 
al. (1984) indicated that simplified mathematical formulations were implemented in order to 
make the model computationally efficient. For example, the canal routine developed for this 
model was a mass balance procedure that sums all the inflows and outflows of a canal to 
determine the water surface position at the end of each day. The canals were defined as 
continuous channel reaches with flow control structures at the upstream and downstream 
ends. On the other hand, the overland flow was simplified using a diffusion flow 
approximation based on Manning’s equation. Naturally, this model cannot be expected to 
provide detailed flood routing results for single events, or to define in detail the depression 
cone around municipal wells; but, according to MacVicar et al. (1984) the model did 
simulate regional flooding in undeveloped areas, and also indicated excessive groundwater 
drawdowns when they occurred. 
MacVicar et al. (1984) indicated that the period 1969-1971 was chosen as the calibration 
period because it contained the extremes of severe drought and heavy rainfall within the 
three-year span. The period of 1973-1975 was selected as validation period. The investigators 
reported a good agreement between simulated and recorded water levels at two gages in 
WCA1 (gages 1-8 and 1-7). They reported that evapotranspiration and overland friction 
losses were the two major calibration parameters. Water quality and mass transport were not 
simulated during this study. 
The SFWMM continues to be developed and its period-of-record for simulation extended in 
support water resources management in the South Florida area (SFWMD 2003). A 
companion model, the Natural Systems Model (NSM), also continues in development. The 
NSM is essentially the SFWMM with manmade alterations of the system (e.g. canals, levees, 
water control structures) removed, and topography restored to an estimate of pre-
development conditions. The NSM has provided a basis for some restoration targets but its 
application remains a source of controversy . 

• Richardson et al. (1990) studied the distribution of water over space and time, and how 
vegetation was being structured on the Refuge by hydroperiod pattern. A hydrologic model 
was developed to better understand the hydrologic characteristic of the Refuge. For this task, 
topographic data was gathered at a resolution of approximately 1 minute of latitude and 
longitude. Data recorded at each site included water depths, and percent cover by each 
vegetation class. Elevations were determined by measuring the water depths at all of the grid 
locations and then subtracting from an assumed horizontal water level. A flat pool condition 
of water in the Refuge was obtained by holding water at the 17 foot level during the time that 
the grid survey was being conducted. 
A hydrologic simulation model was constructed utilizing the Adaptive Environmental 
Assessment Everglades Simulation Model (AEA Everglades Model) developed by Carl 
Walters (Walters, 1990; Tait, 1990). Among the modifications to the AEA Everglades model 
to make it applicable to the Refuge, are: 1) the cell size was reduced from 4000 meters to 
about 915 meters (3,000 ft.), 2) the roughness coefficient used in the Manning equation to 
calculate fluxes between cells were adjusted to the new grid size, 3) rainfall data for the 
Refuge (from SFWMD) were substituted for South Florida rainfall, and 4) the cells along the 
edge that were influenced by the rim canal were tagged in the model as canal cells. The stage 
of the rim canal was not modeled but used as a boundary. The input and output to the canal 
were controlled using the historic monthly canal levels (data form SFWMD) by adjusting the 
water depths in canal cells. 
A 16 years period, 1970 through 1985, represented the standard base run of the model. The 
simulations were compared to two stage stations, one approximately in the center of the 
Refuge (gage 1-7) and the other in the south-east portion of the Refuge (gage 1-9). Recorded 
data indicated that, during the 192 month time period, there were 33 and 11 months of 
drawdown at the 1-7 and 1-9 gages respectively. With water depths smaller than 0.075 feet 
set as dry, it was predicted there were 30 months of drawdown at the 1-7 gage and 14 months 
of drawdown at the 1-9 gage. The model slightly underestimated the 16-year hydroperiod for 
the central gage and slightly overestimated the hydroperiod at the southeast gage. The R2 
values were 0.75 and 0.83 for water levels at gages 1-7 and 1-9, respectively. The model was 

later used for approximating spatial hydroperiods for the Loxahatchee Refuge. Estimates of 
water depth, variance in water depth, hydroperiod, variance of hydroperiod, and water 
surface elevations for each monthly time period over the 16 year simulation were obtained 
for each of the 750 grid cells. The 16 year hydroperiod over the entire Refuge ranged from 
70% to 98% (wet period over total period) exhibiting an obvious north-south trend of 
increasing hydroperiod with localized anomalies corresponding to topographic features. 
Mean water depth for the study period ranged from 0.2 ft. in the north end to 3.2 ft. in the 
south. It was found that the north end of the Refuge had much greater variance in 
hydroperiod than the south end. Richardson et al. (1990) stated that during dry years, the 
north end of the Refuge is much more susceptible to staying dry for long periods, while in the 
south the dry season is not as likely to completely dewater the marsh for months at a time. 
• Raghunathan et al. (2001) developed the Everglades Water Quality Model (EWQM) to 
predict phosphorus (P) fate and transport in the Everglades. The Water Conservation Areas 
and the Everglades National Park (ENP) were included in the model. The output from the 
SFWMM was used to transport phosphorus between model cells and canals. As in the 
SFWMM, the model used 2 x 2 mile grid-cells. A simplified relationship based on a single 
apparent net settling rate coefficient was used to represent the combined effect of all 
biogeochemical processes that control the dynamics of phosphorus in the water column. This 
simplified relationship indicated a net deposition of phosphorus in the sediments. An 
apparent net settling rate equal to 6.30 m/year was found for WCA-1 during the calibration 
period. The model simulation period extended from 1979 to 1989. Model results indicated 
that the interior of WCA-1 exhibits much lower concentration than the areas near the rim 
canal. However, the rim canal was simulated with a single water quality segment without 
nutrient concentration gradients (the EWQM assumed a constant canal water depth of 3m). 
Model results also suggested that reduction of P concentrations leaving the EAA will result 
in lower concentrations entering the Everglades National Park (Raghunathan et al. 2001). 
Even though a good tool for screening the effects of nutrient reduction options in the regional 
scenario of the EAA-WCAs-ENP system, this model lacks the level of details necessary to 
accurately model the phosphorus dynamic, and the temporal and spatial distribution of water 
within the Loxahatchee Refuge. 

• Welter (2002) used the Regional Simulation Model (RSM) to simulate the hydrology of the 
Loxahatchee Refuge. The model used a grid with 16,292 triangular cells with average 
element size of 650 ft. Overland, canal, and groundwater flows were modeled. Welter (2002) 
expressed that the groundwater portion of the model was simplified as much as possible, 
since the overland processes seems to be more important. Welter (2002) indicated three 
reasons for this approach: 1) the RSM was currently a single layer model and could not 
simulate vertical head gradients; 2) there were no ground water stations in the interior of the 
Refuge (i.e. there were no sufficient information for calibrating a model, and even if the 
model simulated vertical exchange, it could not be calibrated); 3) previous work by Miller 
(1988) and the SFWMD suggested that groundwater processes are much less important than 
the surface water processes. 
The RSM was calibrated over the period of record of 1988 and 1990, and verified for the 
four-year period, 1991 to 1994. The model results showed the same trends observed in the 
field measurements. However, some deviations were observed. Welter indicated that “the 
most disappointing aspect of these results is that measured data shows a larger slope in the 
canal’s water level than the model calculates”, he attributed this discrepancy to inaccurate 
cross section data which, according to him, overestimated depths. He also expressed that “the 
limiting factor in this modeling effort is the sparse network of stage monitoring stations in 
the Refuge”. Welter (2002) indicated that most of the stations are in the perimeter canal, and 
that the only stations in the marsh areas are the 1-7, 1-8 and 1-9 water recorders. Water 
quality and mass transport were not simulated during this study. To the best of our 
knowledge, and at the time of writing this report, the water quality module of the RSM is in 
development and is not currently available. 
• Munson et al. (2002) developed the Everglades Phosphorus and Hydrology (EPH) model to 
simulate water movement and phosphorus dynamics in the water that flows from the EAA 
through WCAs and into the Everglades National Park. The EAA-WCAs-ENP system was 
modeled as a series of cells with water flowing from one cell to the next, using a monthly 
time step. In this application the Loxahatchee Refuge was modeled with only three cells, cell 

1 had a surface area of 250 ha. representing the rim canal, cell 2 had a surface area of 46,952 
ha. representing the north-central portion, and cell 3 with 11,734 ha. represented the southern 
part of the Refuge. The hydrologic processes simulated by the EPH model included 
precipitation, evapotranspiration, inflow and outflow. Total phosphorus in the water column 
was the only nutrient modeled in this application. 
Evapotranspiration parameters and stage-discharge relationship were adjusted during the 
calibration process to obtain the best results for flows and water surface elevations. The 
period of record of 1980-1988 was used for this purpose. The phosphorus removal rate in 
each cell was adjusted in order to match simulated and observed concentrations. During the 
calibration, the average deviations between simulated and observed values for water depths 
and phosphorus concentrations were 7 and 6%, respectively. The model was later applied to 
simulate the impacts on annual average total P concentrations in each cell as a result of the 
implementation of the management plan mandated by the Everglades Forever Act. Model 
results indicate that reductions in input P concentrations will have little impact on P 
concentrations for 85% of the area of the WCAs and on the water entering the ENP. 
• Fitz et al. (2002a) presented the calibration of the Everglades Landscape Model (ELM) to 
match the observed data on water stages and total phosphorus concentration in the water 
column at about 60 point locations distributed throughout the greater Everglades using a 1 
Km x 1 Km square grid. ELM simulates surface, canal and groundwater flow, but it only 
considers advective flow (dispersion is not modeled). Cell surface and groundwater flows are 
solved using a finite difference, Alternating Direction Explicit (ADE) technique, providing 
for propagation of water and water-borne constituents across space. The simulation of 
phosphorus cycles includes uptake, remineralization, sorption, diffusion, and organic soil 
loss/gain. Sixty gages were used for the calibration of water stages (during the period from 
1979 to 1995), but only three gages were located inside the Loxahatchee Refuge (gages 1-7, 
1-9 and 1-8T). The water quality data used in the calibration was total phosphorus (TP) 
concentration sampled in the surface water column during the period from 1979 to 1995. Of 
57 monitoring sites, 21 were located inside the Loxahatchee Refuge. A goodness of fit 
statistic indicated that for water levels, the ELM simulated values explained 68% of 

variability in observed values. While for surface phosphorus concentrations, the results were 
poorer, with an overall R2 of 0.10 for the individual simulated versus observed pairs. When 
weighted seasonal means were used, the average R2 improved to 0.20. When each simulated 
and observed weighted-seasonal mean surface water TP concentration (at all stations) were 
compared, simulated values explained more than 50% of variability in observed values (Fitz 
et al., 2002a). However, differences close to ten orders of magnitude could be found at 
specific locations. It should be noted that the model was not validated. The authors claimed, 
“in our opinion, we do not have to validate the ELM. To build confidence in the models’ 
utility we only need to demonstrate that it performs in a manner consistent with objective” 
(Fitz et al., 2002b). The authors (Fitz et al., 2002b) also stated “ELM is not currently 
intended for application by any individual other than the developers”. At the time of writing 
this report, and to the best of our knowledge, the ELM model has not been validated for the 
Refuge nor has been used by any research group other than the developers. 
• The U.S. Army Corp of Engineers utilized the RMA-2 finite element model to evaluate the 
discharge impacts of S-362 pump station outflow into the Refuge (SFWMD, 2004; Ferguson, 
2002). The model only considered the area of the Refuge immediately adjacent to the S-362 
pump station. It predicted, under various discharge scenarios, velocities at the junction of the 
L-40 canal and the S-362 discharge canal and velocity contours entering the Refuge. 
According to the SFWMD (2004), 1953 as-built cross sections of the L-40 borrow canal 
were used in the RMA-2 model simulations. The predicted velocities at the junction of the 
L40 and S-362 discharge canal were 0.1, 0.2 and 0.8 feet per second for a discharge of 550, 
960 and 4200 cfs, respectively. 
2.2. Previous Modeling Effort in other Wetland Systems 
Several researchers have developed simulation models of the processes associated with wetland 
systems. A wide variety of hydrologic/hydrodynamic models have been used in conjunction with 
water quality models to evaluate the transport, removal and fate of nutrients in these shallow 
water environments. The hydrologic/hydrodynamic models used for simulating wetland systems 
range from simple empirical relationship (Kadlec and Hammer,1982) and simple hydrologic 
models (Mitsch and Reeder, 1991; Walker, 1995; Wang and Mitsch, 2000) to more sophisticated 
hydrodynamic models (Guardo and Tomasello, 1995; Martin and Reddy, 1997; Tsanis et al., 

1998; Moustafa and Hamrick, 2000; Raghunathan et al., 2001; Munson, 2002; Fitz et al. 2002a; 
Meselhe and Douet, 2002). Similarly, the level of complexity on the water quality modules is 
also variable among the different models and applications. This section provides an overview of 
previous modeling effort on wetland systems that were not described in the previous section. 
Kadlec and Hammer (1982) presented a theoretical paper discussing the transport of pollutant in 
wetland systems. They indicated that water flow in wetlands ecosystems, usually occurs in thin-
sheet flows at slow rates, which are controlled by the ground slope, water depths, type of 
vegetation and by the degree and type of channelization. Kadlec and Hammer (1982) indicated 
that removal rates in wetland systems are fast in comparison to typical biological processes, and 
can be represented by a first-order reaction. They conclude that the velocity of the reaction 
suggest a rapid capture mechanism such as adsorption. Kadlec and Knight (1996) also suggested 
nitrogen and phosphorus removal in wetland systems can be approximated by first-order models. 
They indicated that corrections need to be made to account for non-ideal flow, infiltration, and 
atmospheric inputs and outputs. Mitsch (1988) and Mitsch and Reeder (1991) stressed the 
importance of developing a proper hydrologic model as the first step in producing a productivity 
and/or nutrient mass balance simulation. Mitsch and Reeder (1991) developed a hydrologic-
nutrient removal model to estimate the fate of phosphorus in a wetland area adjacent to Lake Erie 
(one of the North American Laurentian Great Lakes). The only state variable in the hydrologic 
model was the volume of water in the marsh, which was affected by rainfall, inflow, 
evapotranspiration and outflow. The TP model included incoming phosphorus, macrophyte and 
plankton uptake, and sedimentation and resuspension of phosphorus. The calibration of the TP 
model was done by varying a resuspension coefficient until the model predicted phosphorus 
concentrations similar to field data. They also modeled plankton and macrophyte biomass 
productivity. Wang and Mitsch (2000) used a similar model to the one presented by Mitsch and 
Reeder (1991) for the evaluation of phosphorus dynamics in created riparian wetlands. The 
hydrology module was updated to include seepage, and bank storage in the water volume 
balance calculation, and periphyton community was included in the productivity model. The 
authors indicated that simulated TP concentrations did not follow observed data well especially 
during no outflow or low flow periods. They expressed that it was due to the fact that the model 
itself is a steady-state lumped model, unable to capture influences of disturbance and random 

effects such as carp or wind stirring of sediments. The lack of an atmospheric deposition term 
may have also introduced errors in the phosphorus budget calculations. 
Walker (1995) presented the development of a mass-balance model for predictions of long-term-
average phosphorus removal in Water Conservation Area 2. The model was driven by inflow 
volumes, precipitation, evapotranspiration, phosphorus loads in the influent and by atmospheric 
deposition, and a calibrated first-order settling rate. Walker (1995) concluded that a settling rate 
of 8.9 to 11.6 m/yr was supported by peat-accretion and water column data. He stated that, over a 
long time period, accumulation of P in plant biomass approaches zero as the ecosystem matures 
and approaches dynamic equilibrium. 
Martin and Reddy (1997) used a simple two-dimensional hydrodynamic model to evaluate the 
fate and transport of nitrogen (N) in wetlands. Horizontal distribution of N was modeled by 
advective transport, and the vertical distribution was simulated as diffusive flux. The effects of 
precipitation and evapotranspiration were neglected in the model. Nitrogen transformation 
simulated in the model included enzymatic hydrolysis of organic N, mineralization, nitrification, 
NH4-N adsorption/desorption, NH3-N volatilization, denitrification, and vegetative assimilation 
and decay. The N processes, with the exception of vegetative uptake, were modeled using first-
order kinetics. In this study, the diffusive flux was varied over three orders of magnitudes, 
ranging from rates indicative of molecular to turbulent diffusion. They concluded that other 
transport processes of magnitudes greater than molecular diffusion account for the transport of 
soluble N in wetland systems. Martin and Reddy (1997) proposed that the turbulent diffusion 
was augmented by vegetation induced water movement, i.e., drawing of water towards the roots; 
however, such explanation does not seem satisfactory to explain an increase of three orders of 
magnitude in the molecular diffusion. A fully dynamic 2-D depth average hydrodynamic model 
was used by Tsanis et al. (1998) to predict phosphorus and suspended solids concentrations in a 
marsh area (Cootes Paradise). They modeled the eddy diffusivity as a constant-isotropic value 
equal to 0.1 m2/s. They used a simplified phosphorus model based on a sedimentation loss term 
that yielded partially good results. Even though the predicted and measured average values, for 
the total study area, were very similar; important differences were observed in discrete 
concentration for specific sites. 

Guardo and Tomasello (1995) also used a fully dynamic 2-D depth average hydrodynamic 
model. They applied the SHEET2D model to the Florida’s Everglades Nutrient Removal (ENR) 
Project. The ENR project contained 3815 acres limited at the east by WCA1, simulated in the 
application by a constant grid size of 600 by 906 feet. Guardo and Tomasello (1995) stressed the 
importance of wetland vegetation in hydrodynamic modeling. They stated that vegetation 
influence hydrologic conditions by consolidating the soil to protect against erosion, trapping 
sediments, building peat deposits, interrupting water flows, and changing flow paths. They also 
indicated that the capability of a model to simulate and predict water quality depends on its 
ability to simulate the relevant hydrodynamic processes. Guardo and Tomasello (1995) indicated 
that a limitation in the modeling effort was the fact that SHEET2D was constraint for a constant 
grid size, they observed that a variable-sized grid network is required for a better representation 
of channels, and in areas where steep topographic gradient exist, such as between the marsh and 
canal bottoms. The hydrodynamic of The Everglades Nutrient Removal (ENR) Project was also 
modeled by Moustafa and Hamric (2000). They applied the Everglades Wetland Hydrodynamic 
Model (EWHM), a version of the 3-D environmental fluid dynamic code (EFDC), to the ENR 
project in two dimensions (i.e., depth-averaged mode). Wind forcing, rainfall and ET were 
applied uniformly to the surface layer over the entire domain, and seepage from WCA 1 was 
estimated following Prymas (1997), and distributed evenly along the L-7 boundary levee. An 
interesting feature of the model is that the effect of submerged and emergent vegetation was 
incorporated into the turbulence closure model and flow resistance formulation, which is 
dependent of plant density. In fact, Moustafa and Hamrick (2000) indicated that, based on the 
vegetation resistance features, the model had no parameters to adjust and it was readily 
calibrated. The EWHM calibration to the ENR Project included comparison between predicted 
and observed water surface elevations, and between modeled and observed chloride (Cl) 
concentrations (no velocity measurements were available at interior sites). According to 
Moustafa and Hamrick (2000) the Cl comparison provided an additional assurance that modeled 
transport of a conservative tracer was accurate. R2 values between 0.79 and 0.84 were reported 
for predicted and observed water levels at different locations, and the authors also claimed that 
modeled and observed Cl data showed a good agreement. In a comment to the Moustafa and 
Hamrick (2000) modeling effort, Kadlec (2002) stated, “Moustafa and Hamrick (200) were quite 

satisfied that their model was successfully calibrated to depth data. But their tracer transport 
predictions are now known to be badly in error”. 
Recent works in modeling wetland areas have been presented by Welter (2002), Ferguson 
(2002), Munson (2002), Fitz et al. (2002a), Meselhe and Douet (2002, 2003 and 2004), and 
Saiers et al. (2003). The work of Welter, Ferguson, Munson, and Fitz et al. is directly related to 
the Loxahatchee Refuge and was detailed in the previous section. Meselhe and Douet (2002) 
presented the application of the 3-D hydrodynamic model, H3D (Stronach et al., 1993) to predict 
water levels variations, and salinity fluctuations in the Brown Lake of the Calcasieu-Sabine 
Basin. The modeling area contained approximately 2,800 acres of wetlands, consisting of 
vegetated marsh and open water. The local model was coupled with a 3-D model of the entire 
Calcasieu-Sabine Basin (Meselhe and Noshi, 2001) which provided boundary conditions for the 
project area. The model was calibrated and validated against observed water level and salinity 
data. The comparison between field measurements and predicted values showed good agreement. 
The calibrated/validated model was then used to evaluate the feasibility of a wetland restoration 
project designed to reduce tidal fluctuations, flooding durations and salinity level within the 
project area. Meselhe and Douet (2003) studied the freshwater introduction into the eastern 
central portion of the Rockefeller State Wildlife Refuge in South Louisiana. They realized that 
water movement through the brackish marsh area was dominated by channel flow rather than 
through sheet flow across the area. Meselhe and Douet (2003) set up a channel network within 
the numerical domain and used the 1-D hydrodynamic model Mike 11 to perform the hydraulic 
calculations, accounting for storage capacity of adjacent marsh, hydraulic structures and salinity 
transport. They calibrated and validated the model for water level and salinity concentrations, 
and reported acceptable agreement between predicted and observed values. They applied the 
calibrated model to evaluate the salinity distribution in the project area under different 
management scenarios. 
Saiers et al. (2003) conducted a tracer experiment at a wetland in the Florida Everglades, and 
compared the measured surface-water transport of inorganic particles with a 3-D transport 
model. Their results indicated that longitudinal, lateral and vertical diffusion were small, and 

nearly equal to 0.16, 0.15 and 0.001 m2/h, respectively. The mean surface-water velocity was 
estimated to be equal to 5.3 m/h. 
Meselhe and Douet (2004) evaluated the effectiveness of the “West Pointe a la Hache Outfall 
Management Project” in the reduction of the Barataria Basin wetland loss rate. The proposed 
project is intended to diminish wetland loss by enhancing the distribution of sediment and 
nutrients, and by reducing saltwater intrusion into the area. Meselhe and Douet (2004) used the 
H3D three-dimensional hydrodynamic model for this task. Actual wind data was used to 
calculate the shear stresses of wind onto the surface water. During the calibration, the authors 
reported that despite “isolated instance of questionable data or unexplained deviations between 
model results and field measurements”, the model presented a good agreement between model 
results and field data for water levels and salinity. After validation, with two additional data sets, 
the model was applied for different simulation scenarios in order to provide an assessment of the 
project features. 

3. OBJECTIVES AND NEED FOR RESEARCH 
According to the Comprehensive Conservation Plan for the Refuge (USFWS, 2000): “Water 
quality, quantity and delivery timing affect the welfare of fish, wildlife and plants…Because the 
Everglades is no longer a free-flowing system that relies on temporal weather patterns to sustain 
it, humans must now attempt to provide water when and where the system can most benefit”. 
The Refuge is impacted by elevated concentrations of nutrients, particularly phosphorus, in 
pumped stormwater. Such nutrients enhance the growth of non-indigenous and invasive species 
to the detriment of native species (USFWS, 2000). Therefore, it is a priority for the Refuge to 
better understand and minimize the impacts of this excessive nutrients loading. Hence, the goal 
of this modeling effort is to provide a quantitative framework for management decisions related 
to Refuge inflow and outflow quantity, timing, and quality. This modeling effort will provide 
projections of water movement and water quality resulting under alternative scenarios of 
structure operation, Stormwater Treatment Area (STA) performance, and structural changes 
within the Refuge. 
When fully calibrated and validated, the selected model(s) should assist in answering questions 
as: 
• What is the impact of different management scenarios on the water distribution inside 
the Refuge? 
• Which management scenario will cause portions of the Refuge to dry out and for how 
long? In other words what is the impact of the management scenarios on the hydro-
period? 
• Does the water depth (duration and frequency) satisfy the needs of plants and 
wildlife? 
• What are the spatial and temporal distributions of phosphorus levels within the 
Refuge? 
• What are the impacts of management decisions and strategies on the water quality? 
• What are the impacts of alternative regulation schedules on the water quantity and 
quality in the Refuge? 
• What are the effects of the surface-groundwater interactions on the Refuge? 
• How does the surface and ground water interact in the Refuge? 

3.1. Project Description 
The project is divided into two phases and nine tasks. The effort in Phase 1 will be focused 
primarily on collecting and organizing the information needed to support model implementation, 
including field measurements, topographic data, aerial maps, etc. Phase 2 of the project is the 
model implementation and application. 
Description of each of the project tasks and a summary table of the project deliverables are 
provided below. 
3.1.1. Phase I: Preparation of Data 
Task 1: Data acquisition and processing 
Task 1 is already completed and is documented in the report by Meselhe et al. (2005). The topics 
included in such report include: 
1.1: Select candidate constituents for modeling
1.2: Select period-of-record 
1.3: Types of data 
1.4: Geographic data – elevation, base map – 
1.5: Hydraulic data – stages and structure flows – 
1.6: Meteorological data – rainfall, temperature, ET, wind – 
1.7: Water quality data – inflow, within, and outflow – 
1.8: Procure and QA all data
1.9: Format data as required
Task 2: Develop boundary condition time series 
Flows and concentrations of all modeled constituents at every inflow structure (boundary 
conditions or BCs) must be estimated and compiled into time-series datasets. Time series will 
also be developed for all outflow structures. This is not necessarily a trivial task. Improvement of 
estimation of complete time-series from measurements taken at single times (grab samples) or 
from composite samples has been identified as a significant source of model uncertainty in the 
ELM calibration (Fitz 2003, Water Quality Team presentation). This task should include 

investigation of alternative approaches and selection of the optimal technique. The task also 
includes using this technique to provide BC estimates for model implementation. 
Task 3: Develop daily water/material budgets for all structures and simple models 
Using time series of flow and concentration, historic daily loads for every structure will be 
calculated over the selected POR. This calculation will be performed for all candidate 
constituents identified in Task 1, including budgets (daily totals) for net inflow and net outflow 
and load of each constituent. These daily budgets will be combined into seasonal and annual 
budgets over the POR for each constituent. Trends in load and retained load (inflow minus 
outflow load) will be examined. Simple net Refuge mass balance models will be developed. 
3.1.2. Phase II: Model Implementation 
Task 4: Selection of model(s) 
Model objectives, needs, and required specifications will be developed. Available models will be 
reviewed. Based on an objective evaluation of how well existing models meet project needs, 
available models will be screened to reduce the list of candidate models. A report will be 
developed and provided to an independent committee tasked with recommending model or 
models selected for implementation. This independent committee will be made up of three or 
more experts selected by DOI. In order to maintain their complete independence, DOI funding of 
costs for committee members’ participation will be contracted separately from modeling support 
contract(s). This report addresses the model selection. 
Task 5: Model implementation 
The selected model(s) computer programming will likely require alteration to adequately model 
selected constituents and meet model objectives. This task will therefore involve computer code 
modification and testing. The model will then be implemented using datasets developed in 
preceding Tasks 1 and 2. 
Task 6: Model calibration and verification 
A preliminary calibration of the hydrodynamic model will be performed using observed stage 
from Refuge interior and canal sites. Calibration of mass transport using a relatively conservative 

constituent (e.g., chloride) may then require additional adjustment of hydrodynamic model 
parameters. Within the Refuge, chloride concentration may be accurately estimated from 
conductivity. Initial conductivity mapping data will be used in model calibration. Calibration of 
other reactive water quality constituents should not make further adjustment of the 
hydrodynamic calibration. Preliminary water quality observations acquired in the monitoring 
phase of this project will be directly or indirectly used for calibration. At a minimum, calibration 
statistics reported by the SFWMD for the SFWMM and ELM will be reported (bias, RMS error, 
r2, and efficiency). Reporting will discuss the adequacy of calibration and verification, 
implications on model uncertainty, and possible mechanisms causing degraded calibration 
statistics. Effectiveness of calibration will be quantitatively measured and reported. At the 
completion of this task, the working model will be installed on a USFWS computer, and training 
provided to USFWS staff sufficient to allow independent model runs to be performed by the 
USFWS staff. 
Task 7: Scenario analysis 
Alternative management strategies will be defined and simulated. Performance measures and 
simple statistics, as well as spatial mapping, will be used in comparison of alternatives. 
Task 8: Documentation 
Full documentation of all tasks of this project is required. Publications in peer-reviewed journals 
will be encouraged and supported. However, peer reviewed publications do not substitute for 
detailed project reporting and exhaustive review by DOI staff and management, SFWMD/COE 
staff, and consultants familiar with the system and project. The standard for project reporting is 
that a professional without specific knowledge of this site or project could implement every task 
of the project using only project reports and without need to consult the modeling staff. Although 
a final report and final documentation will be deliverables, documentation will be required 
throughout the project as an essential part of every task and deliverable. 
At the completion of task 6, a report will be delivered fully documenting task 4-6. Model training 
and training materials will also be provided to interested federal employees following completion 
of task 6. 

Task 9: Archive of program and all other files
All programs, input and output datasets, and reports will be centrally archived in electronic form. 
At project completion, a copy of this archive will be provided to the Refuge.
Table 3. Summary of Project Deliverables 
Due Date 
General 
Monthly activity and progress reports – short (1-page or less) 5th business day of 
following month 
Annual report – year 1 report of progress End of 14th project 
month 
Final completion report In the last month of 
project 
Presentation abstracts and draft publications derived from this When submitted 
project 
Task related deliverables 
PHASE I: PREPARATION OF DATA 
Task 1: Data acquisition and processing 
Task 2: Develop boundary condition time series 
Task 3: Develop daily water/material budgets for all structures Completion of task 3 
and simple models - a report on load methods and estimates over 
POR and simple mass balance modeling for the POR 
A data report fully describing data sources and transformations Completion of 
will be submitted, all data will be archived and documented phase-1 
PHASE II: MODEL IMPLEMENTATION 
Task 4: Selection of model(s) – report supporting model selection Completion of task 4 
including listing and describing candidate models 
Task 5: Model implementation 
Task 6: Model calibration and verification – model Completion of task 6 
documentation report 
Task 7: Scenario analysis – management decision support report Completion of task 7 
Task 8: Documentation – revision of previous reports (if needed), Project completion 
training materials and of model users 
Task 9: Archive of program and all other files – final copies of all Project completion 
computer files including data, input and output files, and 
programs will be transferred to a Refuge computer or server 

4. MODEL SELECTION 
4.1. Candidate Models 
Eighteen models were considered as candidates for this modeling effort. To be included in this 
list, available models had to meet one or more of the following criteria: 
· The model has capabilities for simulating hydrodynamics and transport processes. 
· The model has capabilities for simulating water quality processes. 
· The model is available and documented through manuals, publications and/or user 
guides. 
The Eighteen models or combination of models included in the evaluation are: 
1. MIKE 3 
2. Wetlands/WASP 6 - EFDC 
3. H3D 
4. TELEMAC 
5. MIKE Flood + MIKE SHE 
6. ECOMSED-RCA 
7. SSIIM 
8. ELM 
9. CCHE-2D, -3D, -WQ 
10. SFRSM 
11. MODHMS 
12. FTLOADDS 
13. TABS-MD(RMA2-RMA4) 
14. WQMAP 
15. GSSHA 
16. GEMSS 
17. FVCOM 
18. WASH 123 
4.2. Model Evaluation Sheet 
A model evaluation sheet was designed in order to simplify and standardize the evaluation. 
Each of the identified models was reviewed, and the key information was summarized in the 
respective model sheet (see Appendix A for the model evaluation sheets). 
The model evaluation sheet divides the model information in three major components: 

A) Hydrodynamics 
Spatial Dimension: identifies the spatial dimension of the model, e.g., one dimensional 
(1D), two-dimensional (2D), or three-dimensional (3D) 
Time Dimension: identifies whether or not the model simulates time-varying (unsteady) 
conditions, and what are the limitations, e.g., only daily variations, monthly variations, 
etc. 
Model Characteristics: provides an overview of the hydrodynamic features in the 
models, e.g., what is the numerical method/scheme used in the model. 
Wetting and Drying: identifies whether or not the model is able to simulate flooding and 
drying processes. 
Ground Water Flow: identifies the ability of the model for simulating surface-
groundwater interactions. 
Additional Information: provides additional information about hydrodynamics features 
in the model. 
B) Water Quality 
Components: identifies the main components of the water quality module in the model. 
Vegetation: identifies the type of vegetation included in the water quality module. It 
indicates if the model is able to simulate nutrients plant uptake and plant growth. 
Soil: identifies the ability of the model for simulating nutrients transformation in the soil, 
and soil –water column interactions. At a minimum, models must have the capability of 
simulating a stationary mass compartment that interacts with the surface water column. 
Additional Information: provides additional key information about water quality 
features in the model. 
C) General Information 
Public Availability: identifies the availability of the model for use and distribution. 
Run Time: identifies whether or not it is possible to run long-term simulations with a 
reasonable execution time. It should be emphasized that our judgment is somewhat 
subjective since we did not perform a true comparative testing for all the models in a 
single platform. Therefore, the information listed is based on either on our own 
experience or gathered from developers or users. 

Acceptance: identifies the general acceptance of the model within the professional 
community based on factors such as: prior peer-reviewed publications, adopted by 
agencies or successful applications to similar projects. 
Documentation: indicates the availability of model documentation through user manuals, 
publications and/or other technical documents. 
Pre/Post Processor: indicates the availability of pre/post-processing modules. 
Contact Information: identifies contact person and location information for model 
information, procurement, and technical support. 
Platform: indicates the model platform, e.g., Windows, Linux, etc. 
Technical Support: indicates the availability of technical support for the model. 
Source Code: identifies whether or not the source code is available, and what 
programming language it is based on. 
Other Model Features: provides any key information that was not included in the 
previous sections. 
Other Capabilities: lists additional capabilities that may be important for the Refuge 
application. 
Limitations: summarizes the technical or practical limitations that were not explicitly 
indicated in the previous sections. 
It should be emphasized that it was challenging to collect all the aforementioned information for 
each of the models. For certain models, if the information was not readily available in published 
reports or papers, effort was devoted to personally contact the developers to complete the forms 
as much as possible. We were unable to completely fill the forms for all models. However, we 
believe the information gathered is sufficient and adequate to select a model (or two) for the 
proposed modeling effort. It is important to realize that model development is a continuous 
process, and new models will become readily available. Similarly, some of the models that were 
included might evolve and become more suitable for this application. Although the “perfect” 
model may be an elusive target, migrating to new models with superior capabilities as they 
emerge is recommended. 

4.3. Model Selection Criteria 
It is crucial to ensure that the model selection is guided by the project objectives. A summary of 
the project objectives is provided below: 
• Provide the best available technical support for management decisions related to Refuge 
inflow and outflow quantity and quality. 
• Provide projections of water movement and water quality resulting under alternative 
scenarios of structure operation, treatment performance, and structural changes within the 
Refuge. 
• Provide a quantitative platform for analysis of causes of elevated phosphorus events. 
Based on these objectives, the research team designed the following system to evaluate the 
candidate models. It should be noted that a computer model that fully satisfy all the 
requirements might not be readily available. Therefore, some compromise among the selection 
criteria will almost certainly be required. It is anticipated that some customization and 
formulation improvements will be needed. However, due to time and budget constraints, it is 
highly desirable to minimize code development effort. Based on the project objectives, we 
established essential and desirable features. A summary of the essential and desirable features 
are listed below: 
Essential Features 
• The model must have at least a 2-D (depth averaged) fully dynamic surface flow 
module. A 1-D model is not suitable for this application. A 3-D model may not 
be needed but is not detrimental, unless it severely impacts the execution speed. 
• The model must be able to simulate wetting and drying phenomena. This is a 
crucial component. Since it is challenging to develop and fully test a robust 
module for wetting and drying, any model that does not have such feature 
available should not be selected. 
• The model must have either a water quality module, or at least user-defined 
reactive transport module. 
• The model must include vertical exchange with the groundwater. Although the 
significance of the surface-groundwater interaction is a subject of debate, per the 
Refuge personnel the ability to model such interaction is important. Even though, 

a complete groundwater subroutine is preferred, there are not sufficient data to 
calibrate a horizontal groundwater model. 
• The model must have a surface water module with variable spatial resolution or 
other mechanism to link channel to marsh. 
• The investigators should have at least partial access to the source code to 
implement improvements to the formulation especially to the water quality 
module. 
Desirable Features 
• The model should have good pre/post processing modules. 
• The model should have documentation that includes theoretical background, input 
and output formats, and any pre and post processors. 
• The model should have availability of technical support from developers, 
experienced staff, or other users. 
In summary, the most appropriate model(s) for this project should have as many of essential and 
desirable features as possible in order to minimize the development effort. 
4.4. Preliminary Evaluation Results 
Table 4 shows a comparison for the models relative to the essential and desirable features listed 
above. The table also indicates the number of essential and total criteria met by each model. As 
seen in the table, two points were assigned for each essential feature, while one point was 
assigned for each desirable feature. Models that scored at least 10 points for the essential 
features and 12 points overall were selected for further consideration. These models are: 
• Wetlands/WASP 6 - EFDC 
• H3D 
• TELEMAC 
• MIKE FLOOD 
• SSIIM 
• ELM 
• GSSHA 

· GEMSS 
· FVCOM 
· WASH-123 
Table 4. Model Selection Matrix 
Essential Features Desirable Features 
1 2 3 4 5 6 7 8 9 Summary 
Criteria 
Numberof CriteriaMet2D or 3DHydrodynamicsModel 
Wetting and DryingWaterQuality/TransportModuleGround Water FlowOpen Source CodePre/Post ProcessingDocumentationTechnical SupportChannel flow link tooverland flow orvariable spatialresolutionEssentialTotalConsider Further? 
1 MIKE 3 · · · X X X · · · 6 9 No 
2 
Wetlands/WASP 6 -
EFDC · · · · · • · • 11 13 Yes 
3 H3D · · · • • · • • · 10 12 Yes 
4 TELEMAC · · · • · • · · • 10 12.5 Yes 
5 MIKE-FLOOD · · · • · X · · · 9 12 Yes 
6 ECOMSED - RCA · X · • X · • · · 7 9.5 No 
7 SSIIM · · · ? · · · · X 10 12 Yes 
8 ELM • · · · · · · • • 11 13 Yes 
9 CCHE-2D,- 3D, -WQ · · · ? · ? · · ? 8 10 No 
10 SFRSM • ? · · · • X • ? 8 8.5 No 
11 MODHMS • · ? · • X · · · 6 9 Yes 
12 FTLOADDS · · • · X · • · • 9 11 No 
13 RMA2 - RMA4 · · · ? · • · · · 9 12 No 
14 WQMAP · · · • • • · · · 9 12 No 
15 GSSHA • · • · · · · · · 10 13 Yes 
16 GEMSS · · · • · · · · 10 13 Yes 
17 FVCOM · · · • · · • · • 11 13 Yes 
18 WASH123 · · · · · X · • • 10 12 Yes 
Criterion fully met (two points for essential feature, one point for 
X Criterion is not met (no point)
· 
desirable)
Criterion partially met (one point for essential featurs, half point for
• ? No information
desirables) 

Additional Information about the selected models: 
-Regarding the SSIIM, it has several components that have not been fully tested, and it 
does not have any technical support available. 
-The hydrodynamic module of ELM does not include the longitudinal dispersion process. 
Additionally, the overall evaluation indicates that the complexity of the formulation in 
the ELM model is beyond the scope of the Refuge's modeling project. Accordingly we do 
not recommend considering this model further. However, this model is a valuable 
resource of information regarding modeling of Phosphorus in a wetland system. 
Therefore, we may use some of the formulations in ELM to improve the water quality 
module of the selected model(s). 
-The ELM calibration to Everglades TP data was reported by Fitz et al. (2002a). Other 
comments that reflect negatively on the selection of ELM for this Refuge modeling 
project were expressed during a RECOVER inter-agency review of ELM for application 
in CERP project evaluation (Fitz et al. 2002b). These include: 
o Use of Manning's equation to characterize wetland flow 
o Unsatisfactory calibration statistics and patterns of model bias 
o Large number of parameters and model complexity 
o Concerns regarding the ET formulation in ELM and coupling transpiration with TP 
movement 
o Lack of users manual or other similar documents describing file formats for input and 
output 
-The overland flow module of the GSSHA modeling system is based purely on the 
diffusion approximation. The impact of ignoring advection is unknown at this time. 
- To the best of authors’ knowledge, the run time of the WASH-123 modeling system is of 
concern. The Refuge personnel prefer to run models on their local computers and avoid 
the need to use super computer centers. The run time of WASH 123 might be prohibitive 
especially for decadal simulations. Moreover, the developer indicated that for this 
current application we would be only given the hydrodynamic source code. Therefore we 
will not be able to implement additional capabilities to the water quality module if 
needed. 

Accordingly, the following five models are the most suitable models for the Refuge. 
· FVCOM 
· MIKE FLOOD 
· Wetlands/WASP 6 - EFDC 
· TELEMAC 
· H3D 
· GEMSS 
In order to select the one or two most suitable models for the Refuge from the top five models 
listed above, the following pros/cons table may be considered (See Table 5). 
Table 5. Additional Pros and Cons of Selected Models 
Model Pros Cons 
FVCOM 
(11 - 13) 
1) Unstructured grid 
2) Excellent mass conservation 
3) Fully open code 
4) Fully parallel 
1) New improvement to an 
existing model (ECOMSED) 
2) Requires separate software 
for Post processing. 
3) Might require a minimum 
number of elements to 
adequately represent the 
channel 
4) Not very fast 
Wetlands EFDC 
(11 – 13) 
1) 1D channel to couple with 2D 
overland 
2) Fully open code 
1) Coarse Cartesian grid will 
not capture tree islands 
well. Fine grid is a high 
cost. 
2) Kadlec negatively 
commented on the transport 
module of EFDC 
MIKE FLOOD 
(10 – 13) 
1) 1D channel coupled with 2D 
overland 
2) Good Pre and Pos processing code 
1) The source code is not 
open. 
TELEMAC 
(10 – 12.5) 
1) Unstructured grid 
2) Fully parallel 
3) Good post processing 
1) Not very fast 
2) Source code partially open. 
3) Might require a minimum 
number of elements to 
adequately represent the 
channel 

H3D 
(10 – 12) 
1) Extremely computationally 
efficient 
2) Fully open 
1) Coarse Cartesian grid will 
not capture tree islands 
well. Fine grid is a high 
cost. 
2) Requires separate software 
for Post processing 
3) Stair-casing in the channel 
GEMSS 1) Good pre and post processing 1) To capture the rim canal 
(10 - 13) 2) Fully open and interior tree islands will 
cause curvilinear grid to be 
quite large 
It will be difficult to adequately capture the canal and the canal-marsh interaction using the 
model H3D or GEMSS. Therefore, these models will not be further considered. Also the model 
Wetlands-EFDC will not be further considered, since it was already applied to a similar case and 
the results were not satisfactory. Both FVCOM and TELEMAC present the limitation that a 
minimum number of elements might be needed to adequately capture the channel. Therefore, 
computational time is a concern when using FVCOM or TELEMAC. FVCOM has two important 
advantages over TELEMAC: (1) it is a public domain-fully open source code model and 
TELEMAC is a proprietary model, and (2) the mass conservation properties of the Finite 
Element method used in TELEMAC is a concern, while FVCOM use the Finite Volume method 
which is mass conservative. TELEMAC will not be further considered. 
This selection leaves us with two final candidates: FVCOM and MIKE FLOOD. 
MIKE FLOOD is a model with a proved record of successful applications and is widely 
accepted. MIKE FLOOD can capture the channel and the channel-marsh interaction; however is 
a proprietary-closed source code model. FVCOM is public domain –fully open source code, but 
is a new model with a short record of applications. The research team decided to continue with 
the modeling effort using these two candidate models, i.e., FVCOM and MIKE FLOOD. The 
two models will be set up and further evaluated. Based on model performance, it will be later 
decided whether to continue using the two models or to direct all the efforts in one of them. 

4.5. Resource Models 
The model evaluation team also reviewed a series of models that did not match the selection 
criteria because of their hydrodynamic features. These models include information, especially 
water quality formulation, that can be transferred and used for the Refuge application. Eleven 
models were considered for future utilization as resource models: 
19. DMSTA 
20. CE-QUAL-R1 
21. CE-QUAL-W2 
22. LOWQM 
23. WQRRS 
24. WASP 6 – DYNHYD5 
25. HSPF 
26. RCA 
27. GLEAMS 
28. BLTM 
29. SWAT 
Even though these models are not considered as candidate model for this Refuge application, 
their information was also summarized using the same model evaluation sheet utilized for the 
candidate models. Appendix B shows the Model Evaluation Sheet for the resource models. 

5. SUMMARY 
The effects of different management scenarios on the spatial and temporal distribution of water 
quantity and quality in the Refuge have not been fully quantified and assessed. Therefore, a 
predictive tool that can support management decisions, and provides answer to the questions 
related to water quality, quantity and timing is needed. 
Based on the review of previous modeling efforts in the Refuge, it is clear that the current needs 
have not been adequately addressed. To be specific, these efforts lacked adequate spatial 
resolution, and thorough calibration and validation of water quality parameters. It is also 
important to note that thus far, validation of velocities and transport subroutines have not been 
done primarily due to lack of field measurements. 
None of the models previously implemented for the Refuge address the dynamic interaction 
between the rim canal and the interior. Moreover, interaction between surface and ground water 
was either not simulated or not calibrated. Again, currently there are no field data to calibrate 
such interaction. Therefore, it will be recommended to Refuge personnel to collect surface flow 
velocities in the rim canal as well as in the Refuge interior, and collect data to estimate the 
interaction between surface and groundwater. Overall, previous models have captured the 
general trends, and the monthly-seasonal dynamics (e.g., ELM, SFWMM). However, no model 
has described in detail the internal dynamics in the Refuge. Accordingly, these models are unable 
to provide detailed spatial and temporal information of water quantity and quality within the 
Refuge. 

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Langevin, C., Meselhe, E., and Griborio, A. (2005). FTLOADDS Application – Model 
Capabilities. Personal Communication. 
Langevin, C.D. (2003). Simulation of Submarine Ground Water Discharge to a Marine Estuary: 
Biscayne Bay, Florida. Ground Water, Vol. 41 (6), pp. 758 -771 
Langevin, C.D., Shoemaker, W.B., and Guo, W. (2003). MODFLOW-2000, the U.S. Geological 
Survey Modular Ground-Water Model-Documentation of the SEAWAT-2000 Version with the 
Variable-Density Flow Process (VDF) and the Integrated MT3DMS Transport Process (IMT). 
U.S. Geological Survey, Open-File Report 03-426, 43 p. 
Langevin, C.D., Swain, E.D. and Wolfert, M.A. (2004). Numerical Simulation of Integrated 
Surface-Water/Ground-Water Flow and Solute Transport in the Southern Everglades, Florida. 
U.S. Geological Survey, Open-File Report 2004-1097, 12 p. 
Langevin, C.D., Swain, E.D. and Wolfert, M.A. (2004). Simulation of Integrated Surface-
Water/Ground-Water Flow and Salinity for a Coastal Wetland and Adjacent Estuary. U.S. 
Geological Survey, Open-File Report 2004-1097, 30 p. 
Leonard, R.A., Knisel, W.G., and Still, D.A. (1987). GLEAMS: Groundwater Loading Effects of 
Agricultural Management Systems. Transactions of the ASAE, Vol. 30(5), pp.1403-1418. 
Lumb, A. M., McCammon, R.B., and Kittle, J.L. (1994). Users Manual for an Expert System 
(HSPEXP) for Calibration of the Hydrological Simulation Program-FORTRAN, U.S Geological 
Survey, Water-Resources Investigations, Report 94-4168, 102 p. 
Olsen, N. R. (2004). A Three-Dimensional Numerical Model for Simulation of Sediment 
Movements in Water Intakes with Multiblock Option -SSIIM Model – Version 1.1 and 2.0. 
Department of Hydraulic and Environmental Engineering, The Norwegian University of Science 
and Technology, 141 p. 
Panday, S., and Huyakorn. (2004). A fully coupled physically-based spatially-distributed model 
for evaluating surface/subsurface flow. Advances in Water Resources, 27, pp. 361 -382. 
Panday, S., Meselhe, E., and Griborio, A. (2005). MODHMS Application – Model Capabilities. 
Personal Communication. 
Petranek, J.A., Griborio, A., and Meselhe, E. (2005). RMA Application – Model Capabilities. 
Personal Communication. 
Schaffranek, R. W. (2004). Simulation of surface-water integrated flow and transport in two 
dimensions: SWIFT2D user’s manual. U.S. Geological Survey Techniques and Methods, book 6, 
chap. 1, section B, 115 p. 

SFWMD Consultant Task 2.1.1 (2003). Water Quality Modeling -Reservoir Phosphorous 
Uptake Model. Central and Southern Florida Project, Comprehensive Everglades Restoration 
Plan, January. 
SFWMD Consultant Task 2.2.4 (2004). HydraulicsHydrologic Modeling/Methodology Report. 
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Engine (HSE), Author and Date Unknown, Document obtained from the 
SFWMD website: www.sfwmd.gov/org/pld/hsm/cerp_pres/hse_num.pdf 
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Hydrodynamic-Euthrophication Model (HEM-3D): Application of the Hydrodynamic Model to 
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341, 123 p. 
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Personal Communication. 
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Personal Communication. 
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Simulation Program (WASP) – Version 6.0 – Draft: User’s Manual, 267 p. 

8. APPENDIX A: CANDIDATE MODELS- EVALUATION SHEETS

Model Evaluation Sheet 
Model No. 1: Mike 3 
Component A: Hydrodynamics 
Dimension Spatial: 3D Time: Unsteady 
Model Characteristics Complete hydrodynamic model, implicit ADI finite difference scheme of 2nd order accuracy 
Wetting and Drying Flooding and drying is included Ground Water Flow It is not included 
Additional Information Includes different turbulence models 
Component B: Water Quality 
Components Nutrients and DO/BOD. Basic and extended eutrophication module 
Vegetation Algae, macro algae and benthic vegetation 
Soil Sediment nutrient flux model and sediment diagenesis 
Additional Information Complete N, P and phytoplankton cycles 
Component C: General 
Public Availability Available Contact Information DHI; www.dhigroup.com 
Run Time No information Platform Windows 
Acceptance Wide Technical Support Available 
Documentation Available Source Code Not public 
Pre Processor Available - Included Post Processor Included – animated presentation 
Other Model Features Complete sediment transport module. Transport of suspended substance, including erosion, transport and deposition 
Other Capabilities Modeling the transport of trace and dissolved substance, might include decay 
Simulates heat exchange with the atmosphere, including evaporation and precipitation 
Accepted by the US Federal Emergency Management Agency (FEMA) 
Limitations Proprietary model 

Model Evaluation Sheet 
Model No. 2: Wetlands/WASP 6-EFDC (Environmental Fluid Dynamic Code) 
Component A: Hydrodynamics 
Dimension Spatial: EFDC? 3D Time: Unsteady 
Model Characteristics Complete hydrodynamic model, finite difference Cartesian or curvilinear-orthogonal grid 
Wetting and Drying EFDC can simulate wetting and drying Ground Water Flow Vertical Exchange 
Additional Information Computes changes in surface water elevation and horizontal movement that result from inflows and outflows to and from the wetland 
The hydrodynamics is affected by evaporation and precipitation, The model can include source/sink representing groundwater exchange or can include a soil moisture layer 
Component B: Water Quality 
Components Floating periphyton mat, water column, benthic periphyton mat, detrital litter layer, and a sediment layers. Eutrophication submodel 
Vegetation Uptake by periphyton and emergent vegetation 
Soil Sediment nutrient flux submodel and back flux 
Additional Information Complete N, P and DO cycles. 
Dissolved and particulate nutrients. Includes temperature for WQ control 
Component C: General 
Public Availability Available Contact Information http://www.epa.gov/athens/wwqtsc/html/efdc.html 
John Hamrick, Tetra Tech 
Run Time No information Platform Windows 
Acceptance Wide Technical Support Partial 
Documentation Available Source Code EFDC is available 
Pre Processor EPA BASINS (in development) Post Processor EPA BASINS (in development) 
Other Model Features The Everglades Wetland Hydrodynamic Model (EWHM), a version of EFDC, dynamically coupled 1D channel with 2D overland flow 
Other Capabilities Includes chemical and atmospheric precipitation for P and others (chemical sub-model) 
The vegetation model considers above- and below-ground biomass. Models the interactions between sediment nutrients, plant growth 
and plant nutrient composition 
Limitations Floating and benthic periphyton mats, the litter layer and the sediment layers are fixed in space, and are not influenced by horizontal 
transport, only by vertical diffusion 

Model Evaluation Sheet 
Model No. 3: H3D 
Component A: Hydrodynamics 
Dimension Spatial: 3D Time: Unsteady 
Model Characteristics Complete hydrodynamic-free surface model. Finite difference model, second order accurate in time 
Wetting and Drying Wetting and drying is included Ground Water Flow Vertical exchange 
Additional Information The model is semi-implicit, so that relatively large time steps can be used. H3D economizes in storage by storing only active cells 
The model can use Cartesian or curvilinear-orthogonal grids. The model conserves scalar quantities in flooding and drying process. 
Component B: Water Quality 
Components Dissolved/suspended substances with a source term for reaction. 
Vegetation Algae 
Soil 
Additional Information Eutrophication module 
Component C: General 
Public Availability Available Contact Information J.A. Stronach; stronach@hayco.com. 
E. Meselhe, meselhe@louisiana.edu 
Run Time Computationally Efficient -Fast Platform Windows/DOS/ Linux/Unix 
Acceptance Wide Technical Support Available 
Documentation Partial Source Code FORTRAN - Available 
Pre Processor Partial Post Processor Tecplot output 
Other Model Features Complete sediment transport module and sediment settling module 
Other Capabilities Simulates heat exchange with the atmosphere 
Includes wind and density effects 
Can include dry cells in the computational domain, and passes through the cells to simulate channel flow 
Note Investigators are familiar with the model 
Limitations Tecplot is a proprietary software, but it is not expensive 

Model Evaluation Sheet 
Model No. 4: TELEMAC 
Component A: Hydrodynamics 
Dimension Spatial: 2D, 3D Time: Unsteady 
Model Characteristics Complete hydrodynamic – free surface model. Finite element model 
Wetting and Drying Flooding and drying is included Ground Water Flow Vertical exchange 
Additional Information Different turbulence models are available. The model has the flexibility of an unstructured grid of triangular elements, which 
means that it can be easily refined particularly in areas of special interest 
Component B: Water Quality 
Components Dissolved/suspended substances with a source term for reaction. Includes a eutrophication module 
Vegetation phytoplankton 
Soil Fluxes can be included: flux of erosion, and flux of deposition on benthic conditions 
Additional Information The model has been extended to include reactive processes 
Component C: General 
Public Availability Available Contact Information CHC; www.telemacsystem.com 
Run Time Relatively slow/ Fully Parallelized Platform Windows 
Acceptance Wide Technical Support Available. The response time is slow 
Documentation Available Source Code Partial 
Pre Processor Available - Included Post Processor Included – animated presentation 
Other Model Features Complete sediment transport module and sediment settling module. Includes sediment consolidation 
Other Capabilities Includes wind and density effects 
Simulates heat exchange with the atmosphere 
Can include dry cells in the computational domain 
Note Investigators are familiar with the model 
Limitations Proprietary model 

Model Evaluation Sheet 
Model No. 5: HEM-3D -EFDC 
Component A: Hydrodynamics 
Dimension Spatial: EFDC? 2D, 3D Time: Unsteady 
Model Characteristics Complete hydrodynamic – free surface model. Finite difference model. 
Wetting and Drying Flooding and drying is included Ground Water Flow Vertical exchange 
Additional Information It’s very computationally efficient, it economizes in storage by storing only active cells 
Sigma vertical coordinate system, and Cartesian or curvilinear-orthogonal grid 
Component B: Water Quality 
Components Complete eutrophication model 
Vegetation Algae 
Soil Sediment nutrient flux model and sediment diagenesis 
Additional Information Complete N, P, DO and phytoplankton cycles 
Includes refractory particulate, labile particulate, and dissolved organic P and TPO4 
Component C: General 
Public Availability Available Contact Information Virginia Institute of Marine Sciences; boon@vims.edu 
Run Time No information Platform UNIX or DOS 
Acceptance Wide Technical Support Partial 
Documentation Available Source Code EFDC is Available 
Pre Processor EPA BASINS (in development) Post Processor EPA BASINS (in development) 
Other Model Features Complete sediment transport module. Transport of suspended substance, including erosion, transport and deposition 
Other Capabilities Includes wind stresses and density effects. Includes transport equation for temperature 
The HEM-3D model can be coupled with others hydrodynamic and sediment transport models 
The Everglades Wetland Hydrodynamic Model (EWHM), a version of EFDC, dynamically coupled 1D channel with 2D overland 
flow 
Limitations The WQ model has not been fully tested 

Model Evaluation Sheet 
Model No. 6: Mike Flood 
Component A: Hydrodynamics 
Dimension Spatial: Dinamically couples Mike 11 (1D) with Mike 21 (2D) Time: Unsteady 
Model Characteristics Complete hydrodynamic model, implicit ADI finite difference scheme of 2nd order accuracy 
Wetting and Drying Flooding and drying is included Ground Water Flow It is not included 
Additional Information Mike Flood uses Mike 11 for river hydraulics and Mike 21 for surface water modeling 
Component B: Water Quality 
Components Nutrients and DO/BOD. Basic and extended eutrophication module 
Vegetation Algae, macro algae and benthic vegetation 
Soil Sediment nutrient flux model and sediment diagenesis 
Additional Information Complete N, P and phytoplankton cycles 
Component C: General 
Public Availability Available Contact Information DHI; www.dhigroup.com 
Run Time Platform Windows 
Acceptance Wide Technical Support Available 
Documentation Available Source Code Not public 
Pre Processor Available - Included Post Processor Included – animated presentation 
Other Model Features GIS integration for spatial and temporal analysis 
Other Capabilities Same as Mike 21 
Accepted by the US Federal Emergency Management Agency (FEMA) 
Limitations Proprietary model 

Model Evaluation Sheet 
Model No. 7: ECOMSED-RCA 
Component A: Hydrodynamics 
Dimension Spatial: 3D Time: Unsteady 
Model Characteristics Complete hydrodynamic – free surface model. Finite volume method second order accuracy 
Wetting and Drying It is not included Ground Water Flow Vertical exchange 
Additional Information Good mass conservation properties associated with the discretization scheme. 
Sigma vertical coordinate system, and Cartesian or curvilinear-orthogonal grid 
Component B: Water Quality 
Components Simple and advanced eutrophication, wetland systems (based on coupling with RCA) 
Vegetation Algae (multiple algal groups) 
Soil Includes a sediment nutrient flux subroutine (deposition and resuspension) 
Additional Information Fully closed P and N cycles, complete DO/BOD dynamics 
Component C: General 
Public Availability Available Contact Information HydroQual, Inc.; Hydroqual.com 
Run Time Relatively slow Platform UNIX, LINUX and DOS 
Acceptance Wide Technical Support Available 
Documentation Available Source Code Available, FORTRAN 
Pre Processor Partial Post Processor Tecplot output 
Other Model Features Complete sediment transport module (cohesive and non-cohesive sediment transport) 
Other Capabilities Includes wind stresses and density effects. Includes transport equation for temperature 
Includes heat flux module (including precipitation and evaporation) 
Limitations Tecplot is a proprietary software 

Model Evaluation Sheet 
Model No. 8: SSIIM 
Component A: Hydrodynamics 
Dimension Spatial: 3D Time: Unsteady 
Model Characteristics Complete hydrodynamic free surface model. Finite volume method 
Wetting and Drying Wetting and drying is included Ground Water Flow No information 
Additional Information A control volume method is used for discretization with power law or 2nd order upwind schemes 
SIMPLE method is used for pressure coupling. Can use non-orthogonal grids. Complete turbulence model 
Component B: Water Quality 
Components Transport of up to 20 constituents with source terms for each one 
Vegetation Algae 
Soil Resuspension is included 
Additional Information The model has some prescribed functions for nutrient cycles, and allows flexible modifications 
Component C: General 
Public Availability Available Contact Information Nils R. Olsen; Nils.R.Olsen@nhl.sintef.no 
Run Time No information Platform Windows 
Acceptance Wide Technical Support No 
Documentation Available Source Code Available 
Pre Processor Available - Included Post Processor Available - Included 
Other Model Features Includes a complete sediment transport module with movable bed 
Other Capabilities Includes heat flux module and transport equation for temperature 
Includes gas reaeration at the water surface 
Other Limitations There are relevant-new implemented algorithms that are not fully tested 

Model Evaluation Sheet 
Model No. 9: ELM (Everglades Landscape Model) 
Component A: Hydrodynamics 
Dimension Spatial: 2D Time: Varying 
Model Characteristics The model captured the spatio- temporal dynamics of hydrology. Cell surface and groundwater flows are solved using a finite 
difference, Alternating Direction Explicit (ADE) technique, providing for propagation of water and water-borne constituents across 
space 
Wetting and Drying It is included Ground Water Flow It is included 
Additional Information ELM divides the landscape into a uniform grid of square cells. The ELM supports user specified grid cell resolution 
The hydrology may be driven by daily flow data, using either historical observations, or output from the SFWMM for management scenarios 
Component B: Water Quality 
Components Phosphorus cycles included uptake, remineralization, sorption, diffusion, and organic soil loss/gain 
Vegetation Periphyton biomass and community type, macrophyte biomass and habitat type 
Soil Phosphorus accumulation in the soils 
Additional Information Growth of macrophyte and periphyton communities responds to available nutrients, water, sunlight and temperature 
Component C: General 
Public Availability Available Contact Information SFWMD; www.sfwmd.gov/org/wrp/elm/ 
Run Time Computationally Efficient - Fast Platform Unix, LINUX 
Acceptance Wide Technical Support Limited 
Documentation Partial Source Code ANSI C 
Pre Processor Available Post Processor Available 
Other Model Features Canal/levee can be superimposed on the grid to define the hydrologic basins and provide for rapid flow of water through the system 
Other Capabilities ELM has been applied with a finer grid to adjacent areas to the Loxahatchee Refuge 
Rainfall and saturated hydraulic conductivity can be included for water budget purposes 
Limitations The finite difference is first order accuracy, and dispersion is not simulated 

Model Evaluation Sheet 
Model No. 10: CCHE2D, CCHE3D, CCHE-WQ 
Component A: Hydrodynamics 
Dimension Spatial: 2D depth-averaged, 3D Time: Unsteady 
Model Characteristics Complete hydrodynamic – free surface model. It is based on Efficient Element Method, a collocation approach of the FEM 
Wetting and Drying Flooding and drying is included Ground Water Flow No information 
Additional Information The model strictly enforces the mass conservation within the computational domain through the user of control volume approach 
The model includes different turbulence closure schemes. CCHE3D uses a structured quadrilateral mesh in the horizontal plane 
Component B: Water Quality 
Components Phosphorous and nitrogen cycles, dissolved oxygen balance. 
Vegetation Phytoplankton kinetics 
Soil 
Additional Information CCHE-WQ is a physical and bio-chemical process based module which simulates WQ variables and pollutant transport dynamically. 
CCHE-WQ considers the impacts of environmental factors such as temperature, pH, and salinity on the WQ processes. 
Different sources can be simulated, e.g, multiple point and non-point, and time-varying flow conditions. 
Component C: General 
Public Availability Available Contact Information CCHE University of Mississippi 
http://hydra.cche.olemiss.edu/ 
Run Time No information Platform Windows 95, 98, 2000 and XP 
Acceptance Wide Technical Support No information 
Documentation Available Source Code No information 
Pre Processor Mesh Generator – GUI Post Processor Graphical User Interface (GUI) 
Other Model Features Includes a complete sediment transport module with erodible and non-erodible sub-regions. 
Other Capabilities The roughness of the moveable bed changes due to change in sediment size and change in bed form 
The sediment module includes the curvature effects for sediment transport in bends 
Limitations The CCHE-WQ module is currently being tested using field data 
The GUI for CCHE3D is under development 
CCHE-WQ and CCH3D are proprietary 

Model Evaluation Sheet 
Model No. 11: SFRSM (South Florida Regional Simulation Model) 
Component A: Hydrodynamics 
Dimension Spatial: 2D Time: Dynamic 
Model Characteristics The Hydrologic Simulation Engine (HSE) simulates the hydrology in south Florida, including the canals, structures and levees. A 
weighted implicit finite volume method is used in the HSE to simulate diffusion flow in both overland and groundwater flow 
Wetting and Drying No information Ground Water Flow Included 
Additional Information The model domain is discretized using triangular cells whose walls control the flow rates into the cells based on Manning’s equation 
for overland flow and the Darcy’s equation for ground water flow. 
Component B: Water Quality 
Components Under development, full mass transport not yet available 
Vegetation 
Soil 
Additional Information 
Component C: General 
Public Availability Available Contact Information Randy Van Zee, Hydrologic Systems Modeling Department, 
SFWMD 
http://www.sfwmd.gov/org/pld/hsm/models/sfrsm/index.html 
Run Time Platform UNIX 
Acceptance New Model Technical Support No information 
Documentation Partial Source Code C++ 
Pre Processor Under development Post Processor Under development 
Other Model Features The processes modeled include overland and groundwater Flow, precipitation, evapotranspiration, infiltration, levee Seepage, canal and 
structure flow 
Other Capabilities 
Limitations This model is currently 'under development'. Individual components are being developed independently and are in various stages of 
completion 
This model is designed for regional, long-term applications. Although scalable, performance constraints may impose practical limits on 
the time and space scales. This model is not intended for local-scale decision-making support. 

Model Evaluation Sheet 
Model No. 12: MODHMS 
Component A: Hydrodynamics 
Dimension Spatial: 3D subsurface, 2D surface Time: Dynamic 
Model Characteristics A MODFLOW variant that fully integrates ground water with surface water modeling 
Wetting and Drying Included Ground Water Flow Included 
Additional Information MODFLOW simulates three-dimensional ground-water flow through a porous medium by using a finite-difference method 
MODHMS includes interactions between overland flow, channel flow, and groundwater flow. Overland flow/runoff is characterized by the two dimensional diffusion wave 
approximation to the St.Venant equations governing shallow-water flow. 
Component B: Water Quality 
Components No information 
Vegetation 
Soil 
Additional Information 
Component C: General 
Public Availability Available, proprietary, free to 
federal government 
Contact Information Sorab M.Panday, HydroGeoLogic, Inc. 
http://modhms.com/software/modhms.html 
Run Time No information Platform Windows 
Acceptance Wide Technical Support Available 
Documentation Complete Source Code Not public 
Pre Processor Available Post Processor Available 
Other Model Features The hydrologic cycle is viewed as a fully integrated system with dynamic interactions between all regimes of flow 
Other Capabilities A curvilinear grid option is available to allow for flexible gridding 
Limitations No information 

Model Evaluation Sheet 
Model No. 13: MIKE SHE 
Component A: Hydrodynamics 
Dimension Spatial: 3D subsurface, 2D surface Time: Dynamic 
Model Characteristics 2D, diffusive wave, finite-difference overland flow and 3D, finite-difference groundwater flow 
Wetting and Drying Included Ground Water Flow Included 
Additional Information Surface water simulation using flow-routing methods and water levels calculated by Manning’s equation or specified relationships 
Includes drainage routing to surface water bodies. Can be coupled with Mike 11 for modeling open channel flow 
Component B: Water Quality 
Components Can be coupled with DAISY that is a single column model, which describes all the major processes related to water, carbon and 
nitrogen in an agricultural ecosystem. 
Vegetation Complete crop model 
Soil Plant uptake of nitrogen 
Additional Information DAISY calculates nitrate and pesticide leaching from agricultural areas 
MIKE SHE can be used to simulate solute transport across the various hydrologic process boundaries 
Component C: General 
Public Availability Available Contact Information DHI; www.dhigroup.com 
Run Time No information Platform Windows 
Acceptance Wide Technical Support Available 
Documentation Complete Source Code DAISY is open source code 
Pre Processor Available Post Processor Included – animated presentation 
Other Model Features Precipitation, evapotranspiration, overland sheet and channel flow, unsaturated and saturated ground water flow are included 
Other Capabilities GIS integration for spatial and temporal analysis 
Weirs, culverts and spillways can be easily modeled using Mike 11 
Limitations Proprietary model 
DAISY does not include phosphorous process 
MIS SHE/DAISY does not model crop and nitrogen processes under flooded conditions 

Model Evaluation Sheet 
Model 14: FTLOADDS (Flow and Transport in a Linked Overland Aquifer Density Dependent System) 
Component A: Hydrodynamics 
Dimension Spatial: 2D (surface flow), 3D (groundwater flow) Time: Unsteady 
Model Characteristics Fully dynamic 2D finite difference for surface water flow, and 3D finite difference for variable-density groundwater flow 
Wetting and Drying Included Ground Water Flow Included 
Additional Information The main linkage between surface and groundwater flow is through a leakage quantity passed between the two models 
Leakage is calculated using a variable-density form of Darcy’s law, the surface water stage, the groundwater head, and a leakage coefficient 
Component B: Water Quality 
Components Tracer mass transport model 
Vegetation 
Soil 
Additional Information 
Component C: General 
Public Availability Available Contact Information langevin@usgs.gov 
Run Time Computationally Efficient - Fast Platform DOS 
Acceptance Wide Technical Support Available 
Documentation Available Source Code Available 
Pre Processor Partial Post Processor Partial 
Other Model Features The model combines SWIFT2D (for overland surface water flow) and SEAWAT (for groundwater flow) 
Other Capabilities SWIFT2D was modified to include rainfall, ET and flow resistance of marsh vegetation 
Recharge and ET are applied to the cells in the uppermost layer in the groundwater model 
The model includes the capability for upward leakage to rewet a surface water cell 
Limitations FTLOADDS has not be linked to a water quality model 

Model Evaluation Sheet 
Model 15: TABS-MD (RMA2 – RMA4) 
Component A: Hydrodynamics 
Dimension Spatial: 2-D depth-average Time: Unsteady 
Model Characteristics RMA2 is a two dimensional, free-surface, depth averaged finite element model for subcritical flow problems 
Wetting and Drying Included (adjust for wetting and drying by element) Ground Water Flow No information 
Additional Information RMA2 computes a FE solution of the Reynolds form of the Navier-Stokes equations for turbulent flows using the Galerkin Method of 
weighted residuals. Friction is calculated with the Manning’s or Chezy Equation, and eddy viscosity coefficients are used to define turbulence characteristics. 
Component B: Water Quality 
Components RMA4 simulates the depth-average advection-diffusion process in an aquatic environment. 
Vegetation Algae (RMA11) 
Soil 
Additional Information It computes concentrations for up to 6 constituents, either conservative or non-conservative using a first order deacy 
The RMA11 (from BOSS Intl.) model may be use to simulate temperature with a full heat exchange with the atmosphere, nitrogen and phosphorous nutrient cycles, BOD-DO, algae, cohesive 
or non-cohesive suspended sediments and other non conservative constituents 
Component C: General 
Public Availability Available Contact Information CHL WES USACE; tabs@hl.wes.army.mil 
BOSS International; www.bossintl.com 
Run Time No information Platform Windows 
Acceptance Wide Technical Support Available 
Documentation Available Source Code FORTRAN 77 - Partial 
Pre Processor Available Post Processor Available 
Other Model Features It can use one-dimensional networking for channels in conjunction with the two-dimensional finite element formulation 
Other Capabilities The model has the flexibility of an unstructured grid of triangular elements 
Models up to 5 different types of 1D flow control structures (2D structures are also permitted) 
Can be linked with the sediment transport model SED2D 
Limitations The model does not allow for baroclinic calculations 
Simple turbulence models: direct value, by Peclet number, and by Smagorisky coefficient. 

Model Evaluation Sheet 
Model 16: WQMAP 
Component A: Hydrodynamics 
Dimension Spatial: 3D Time: Unsteady 
Model Characteristics Finite Difference model that solves the water mass and momentum equations on curvilinear grid to predict a dynamic field of surface 
elevations and velocities. The exterior mode is solved using a semi-implicit solution technique. The interior mode is solved explicitly 
Wetting and Drying It is included Ground Water Flow Vertical exchange 
Additional Information Environmental forcing includes tides, winds, river flows and density distributions 
The basic model is configured to run in a vertically averaged fully dynamic mode. As an option, a full three-dimensional, coupled prognostic, baroclinic version of the model 
can be incorporated. A sigma coordinate transformation on the vertical are applied to the governing equations 
Component B: Water Quality 
Components Pollutant transport model and WASP eutrophication model 
Vegetation Phytoplankton 
Soil The vertically averaged version is configured with one water column layer and a sediment layer 
Additional Information Complete N and P cycles, DO balance 
Component C: General 
Public Availability Available Contact Information Applied Science Associates, Inc. (ASA); 
www.appsci.com 
Run Time Computationally efficient Platform Windows 
Acceptance Wide Technical Support Available 
Documentation Available Source Code Partially available 
Pre Processor Available - Included Post Processor Available - Included 
Other Model Features Integrated Geographic Information System (GIS) 
Other Capabilities The transport equation may included a first order decay coefficient and settling 
Surface heat exchange is included 
Limitations It is a proprietary model 

Model Evaluation Sheet 
Model 17: GSSHA 
Component A: Hydrodynamics 
Dimension Spatial: 2D (surface flow), 2D (groundwater flow) Time: Unsteady 
Model Characteristics The overland flow is based on a 2-D lateral diffusive wave. The model uses a Cartesian grid 
Wetting and Drying It is included Ground Water Flow It is included 
Additional Information Channel routing is also simulated using an explicit solution of the 1-D diffusive wave equation 
The Manning formula is used to relate flow depth to discharge 
Component B: Water Quality 
Components Transport by advection-dispersion and first order reactions in both the overland and the channel modules 
Vegetation 
Soil 
Additional Information 
Component C: General 
Public Availability Available Contact Information Barbara Parsons, 
http://chl.wes.army.mil/software 
Run Time Fast, except when simulating unsaturated 
zone with Richard’s equation 
Platform Windows, Unix, Linux 
Acceptance Wide Technical Support Available 
Documentation Available - Complete Source Code Available 
Pre Processor Available Post Processor Available 
Other Model Features Precipitation, infiltration, evapotranspiration, unsaturated and saturated ground water flow are included 
Other Capabilities Can simulate sediment transport on both the overland flow plane and within the stream channels 
Soil moisture in the unsaturated zone can be simulated using the Bucket method or the Richard’s equation 
Limitations Simplified representation of cross section geometry 

Model Evaluation Sheet 
Model 18: GEMSS 
Component A: Hydrodynamics 
Dimension Spatial: 3D Time: Unsteady 
Model Characteristics Fully dynamic 3D finite difference semi-implicit hydrodynamic model 
Wetting and Drying It is included Ground Water Flow Vertical exchange 
Additional Information Different turbulence models are available. The grid generator module allows the user to create both rectilinear and boundary fitted 
grids 
Component B: Water Quality 
Components I can be coupled with EPA supported EUTRO5 that simulates the interaction of eight water quality state variables, i.e., the dissolved 
forms of ammonia nitrogen, nitrate nitrogen, inorganic phosphorus, carbonaceous BOD, organic nitrogen, organic phosphorus, 
phytoplankton and dissolved oxygen 
Vegetation Phytoplankton kinetics 
Soil It allows sources and sinks of NH3 and DO from and to the sediments 
Additional Information Complete P and N cycles 
Component C: General 
Public Availability Available Contact Information J.E. Edinger Associates, Inc.; www.jeeai.com 
Run Time Computationally efficient Platform Windows 
Acceptance Wide Technical Support Available 
Documentation Available Source Code Available 
Pre Processor Available - Included Post Processor Available - Included 
Other Model Features The modules are embedded in a geographic information and environmental data system (GIS) 
Other Capabilities It includes a sediment transport module 
Surface heat exchange, wind shear and surface precipitation/exchange are included 
Limitations The GEMSS is proprietary, however a free version is available for academic and research purpose 

Model Evaluation Sheet 
Model No. 19: FVCOM 
Component A: Hydrodynamics 
Dimension Spatial: 3D Time: Unsteady 
Model Characteristics 3D, unstructured grid, finite volume, free surface coastal ocean model 
Wetting and Drying It is included Ground Water Flow Vertical exchange 
Additional Information Uses a triangular-unstructured grid. The model has good mass conservation properties associated with the discretization scheme. 
Sigma vertical coordinate system. Mellor and Yamada level-2.5 turbulent closure submodel 
Component B: Water Quality 
Components Phosphorus-Controlled Lower Trophic Level Food Web Model, and WASP-EPA adapted water quality module 
Vegetation Small phytoplankton and large phytoplankton 
Soil The benthic flux from sediment resuspension 
Additional Information Nitrogen, phosphorous and oxygen cycles are included 
Component C: General 
Public Availability Available Contact Information Dr. Changsheng Chen1; c1chen@umassd.edu 
Run Time No information/ Parallelization is available Platform Linux/Windows 
Acceptance New Model Technical Support Available 
Documentation Available Source Code Available, Fortran 90 
Pre Processor Partial Post Processor Tecplot output 
Other Model Features Includes heat flux and precipitation/evaporation modules 
Other Capabilities Includes wind stresses and density effects. Includes transport equation for temperature and salinity 
Includes Sediment Suspension and Tracer-Tracking Models 
Limitations Tecplot is a proprietary software 
It requires a grid generation software 

Model Evaluation Sheet 
Model No. 20: WASH123 
Component A: Hydrodynamics 
Dimension Spatial: 2D (surface flow), 2D (groundwater flow) Time: Unsteady 
Model Characteristics Fully dynamic 3D groundwater flow, and fully dynamic (full Saint Venant Equations) for 1D channel flow and 2D overland flow 
Wetting and Drying No information Ground Water Flow It is included 
Additional Information Galerkin Finite Element Method for solving the 3D Richard’s Equation for variably saturated flow and Lagrangian-Eulerian Finite 
Element Method for solving the 2D full Saint Venant Equations for overland flow. The model utilizes an unstructured mesh 
Component B: Water Quality 
Components It includes a generic water quality module. Transport of dissolved substance in surface and ground water is included 
Vegetation 
Soil Deposition and resuspension is simulated as well as interaction of chemical with bed and suspended sediments 
Additional Information The model contains a comprehensive and generic component for chemical transformation on the groundwater flow, capable of 
simulating multispecies reaction and interactions 
Component C: General 
Public Availability Available Contact Information Dr. Gour-Tsyh Yeh;'gyeh@mail.ucf.edu 
Run Time Slow Model/ Parallelization is available Platform Windows 
Acceptance Wide Technical Support Partial 
Documentation Partial Source Code Available 
Pre Processor Available Post Processor Available 
Other Model Features The model chooses between the kinematic, the diffusive, or the dynamic wave approximation depending on the elements’ conditions 
Other Capabilities Interactions between groundwater, channel and overland flows are accomplished through a mass conservative iterative procedure 
Includes Sediment Transport capabilities 
Includes heat flux and precipitation/evaporation modules 
Limitations Long execution times reduce the practicality of the model for multiple year simulations using single processor machines 

9. APPENDIX B: RESOURCE MODELS - EVALUATION SHEETS

Model Evaluation Sheet 
Model No. 21: DMSTA (Dynamics Model for Stormwater Treatment Areas) 
Component A: Hydrodynamics 
Dimension Spatial: 1D longitudinal Time: Daily variations 
Model Characteristics Simple Hydrodynamic Model; uses wetland treatment cells divided in CFSTRs for reaction. Includes simple reservoir model 
Wetting and Drying Dry out frequency and supplemental water needs Ground Water Flow Seepage in - out 
Additional Information Can Simulate up to 6 cells 
Water Balance: In flow, bypass, rainfall, ET, outflow, seepage in-out 
Component B: Water Quality 
Components Phosphorus (P), P load reaction of wetlands 
Vegetation It is included. Parameter estimation for various types 
Soil 
Additional Information The phosphorus removal performance of stormwater treatment areas (STAs) have been evaluated using DMSTA 
Can not model P removal by particle settling, biological uptake and net refractory biomass storage, or chemical precipitation. Can not model release of P from sediments. 
Component C: General 
Public Availability Available Contact Information William Walker; wwwalker.net/dmsta 
Run Time Computationally Efficient - Fast Platform Excel 
Acceptance Wide Technical Support No information 
Documentation Available - Complete Source Code Available 
Pre Processor Excel Spreadsheet/macros Post Processor Spreadsheet 
Other Model Features Currently used in the evaluation of STAs. 
Other Capabilities Easy to use, simple dynamics with limited number of parameters 
Calibrated to a very large number of wetland systems similar to the refuge 
Limitations 20% standard error for predicted outflow TP 

Model Evaluation Sheet 
Model No. 22: CE-QUAL-R1 
Component A: Hydrodynamics 
Dimension Spatial: 1D vertical Time: Varying 
Model Characteristics Simple hydrodynamic model. Flux model with vertical sequence of horizontal layer 
Wetting and Drying It is not included Ground Water Flow Possible 
Additional Information Simulation of surface flows, interflows and underflow are possible 
Component B: Water Quality 
Components Can model up to 27 variables and 11 materials in sediments, including P, nitrogen (N) and dissolved oxygen (DO) 
Vegetation Phytoplankton and macrophytes 
Soil 
Additional Information Can simulate water quality (WQ) problems associated with reservoir eutrophication 
Complete N & P Cycling models 
Component C: General 
Public Availability Available Contact Information Dorothy Tillman, http://smig.usgs.gov 
Run Time No information Platform Windows 
Acceptance Wide Technical Support Limited 
Documentation Available - Complete Source Code Available 
Pre Processor Available Post Processor Available – Graphics tool 
Other Model Features Good surface heat exchange and DO sub-models 
Other Capabilities Includes anoxic-anaerobic conditions. Uptake-excretion kinetics and regeneration of P and N under both aerobic and anaerobic 
Limitations It is strictly a reservoir model 

Model Evaluation Sheet 
Model No. 23: CE-QUAL-W2 
Component A: Hydrodynamics 
Dimension Spatial: 2D longitudinal - vertical Time: Varying 
Model Characteristics Implicit finite difference (FD) scheme, laterally averaged equations of momentum, continuity and transport 
Wetting and Drying No information Ground Water Flow No information 
Additional Information The model predicts water surface elevations. Used in lakes, reservoirs, and estuaries 
Component B: Water Quality 
Components Can model up to 22 parameters, including P, nitrogen (N) and dissolved oxygen (DO) 
Vegetation Phytoplankton 
Soil 
Additional Information Can simulate water quality (WQ) problems associated with reservoir eutrophication 
Complete N & P Cycling models 
Component C: General 
Public Availability Available Contact Information Thomas Cole; www.wes.army.mil/el/elmodels 
Run Time No information Platform Windows 
Acceptance Wide Technical Support Limited 
Documentation Available - Complete Source Code Available 
Pre Processor Beta Development Post Processor Needs to be developed for graphics 
Other Model Features Multi-branches is possible, variable grid spacing 
Other Capabilities Surface wind stress, long-term simulations 
Hotstart, autostepping 
Limitations Does not include macrophytes 
Requires knowledge of hydrodynamics, chemisty, aquatic biology 

Model Evaluation Sheet 
Model No. 24: LOWQM (Lake Okeechobee Water Quality Model) 
Component A: Hydrodynamics 
Dimension Spatial: One stirred tank plus benthos Time: Dynamic 
Model Characteristics In-lake water movement can be simulated by a separate hydrodynamic model 
Wetting and Drying No information Ground Water Flow No information 
Additional Information 
Component B: Water Quality 
Components Uses WASP to simulate eutrophication in both water and sediments 
Vegetation Algae 
Soil Include sediment resuspension based on hydrodynamic model 
Additional Information Lake water model 
Modified WASP by including three algae groups instead of one 
Component C: General 
Public Availability Under Development Contact 
Information 
Thomas James; tjames@sfwmd.gov 
http://www.sfwmd.gov/org/wrp/wrp_okee/projects/lowqm.html 
Run Time No information Platform Windows 
Acceptance No information Technical Support No information 
Documentation Partial Source Code No information 
Pre Processor WASP interface Post Processor Post-processing graphics routines 
Other Model Features 
Other Capabilities Same WASP capabilities 
Models sediment resuspension 
Limitations Model is currently under development 

Model Evaluation Sheet 
Model No. 25: WQRRS (Water Quality for River-Reservoir Systems) 
Component A: Hydrodynamics 
Dimension Spatial: 1D longitudinal Time: Steady and unsteady 
Model Characteristics One-dimensional representation of reservoirs and the stream hydraulic module routes flow using different methods 
Wetting and Drying It is not included Ground Water Flow No information 
Additional Information 1D representation of well-mixed reservoir and longitudinal conditions in river networks 
Component B: Water Quality 
Components Reservoir and stream WQ modules; can simulate 18 different parameters, including P, N and O 
Vegetation Phytoplankton and benthic algae 
Soil 
Additional Information Can simulate water quality (WQ) problems associated with reservoir eutrophication 
In the stream quality module the rate of transport of quality parameters can be represented for aerobic streams, and peak pollutant loads into the steady or unsteady hydraulic 
environment can be simulated. 
Component C: General 
Public Availability Available Contact Information HEC USACE 
Run Time No information Platform DOS 
Acceptance Wide Technical Support No information 
Documentation Available Source Code No information 
Pre Processor Available Post Processor No information 
Other Model Features Flow and WQ can be simulated for stream network, including branching channels and islands 
Other Capabilities Includes weather data 
Limitations Assumption of completely mixed for reservoirs, requires the assumption of instantaneous dispersion of all inflow quantities 
Present minor errors in mass conservation 
Limited to aerobic systems 

Model Evaluation Sheet 
Model No. 26: WASP 6 – DYNHYD5 
Component A: Hydrodynamics 
Dimension Spatial: DYNHYD5? 1D Time: Unsteady 
Model Characteristics Simple hydrodynamic model, predicts water height and volumes 
Wetting and Drying It is not included Ground Water Flow It is not included 
Additional Information The flow that defines advective transport can be supplied directly or calculated by a hydrodynamic model 
WASP6 might be linked to other 1D, 2D or 3D hydrodynamic models 
Component B: Water Quality 
Components WQ for aquatic systems including both the water column and the underlying benthos. Complete eutrophication module (WASP 
EUTRO module) 
Vegetation Benthos or benthic vegetation, algae 
Soil Benthic fluxes, accumulation in sediments. Sediment diagenesis 
Additional Information Complete N and P cycles, DO balance. Complete phytoplankton model 
Used for WQ problems in ponds, streams, lakes, reservoirs, rivers, estuaries and coastal waters. Used for the development of TMDL 
Component C: General 
Public Availability Available Contact Information EPA; Wool.Tim@epamail.epa.gov 
Run Time Computationally Efficient - Fast Platform Windows 
Acceptance Wide Technical Support Available 
Documentation Available Source Code FORTRAN - Available 
Pre Processor Available - Included Post Processor Included – graphical presentation 
Other Model Features Used for the development of TMDL 
Other Capabilities The eutrophication module can simulate some or all of the parameters 
Includes flux for resuspension of heavy metals 
Can be modified to include other reactions 
Limitations Needs to be linked to a hydrodynamics model 
The sediment diagenesis module is in development 

Model Evaluation Sheet 
Model No. 27: HSPF (Hydrological Simulation Program – FORTRAN) 
Component A: Hydrodynamics 
Dimension Spatial: lumped spatial 2 D Time: Varying 
Model Characteristics Can simulate hydrologic and WQ processes on pervious and impervious surface and in streams and well-mixed impoundments 
Wetting and Drying Partial Ground Water Flow Included 
Additional Information The model produces a time history of the runoff flow rate, sediment load, nutrients and pesticide concentrations 
Overland flow is treated as a turbulent flow process. It is simulated using the Chezy-Manning equation and an empirical expression which relates outflow depth to detention 
storage. The outflow from active groundwater storage is based on a simplified model, it assumes that the discharge of an aquifer is proportional to the product of the cross-
sectional area and the energy gradient of the flow 
Component B: Water Quality 
Components Nutrients cycling in watershed 
Vegetation Allows and optional yield-based method for simulating nutrient uptake by plant 
Soil Land and soil contaminant runoff processes with in-stream hydraulics and sediment-chemical interactions 
Additional Information Includes atmospheric deposition as a mass flux or as concentration in rainfall 
The reaction processes included are hydrolysis, oxidation, photolysis, biodegradation, volatilization and sorption 
Component C: General 
Public Availability Available Contact Information h2osoft@usgs.gov; EPA; epa.gov 
Run Time Computationally Efficient - Fast Platform Windows 
Acceptance Wide Technical Support Limited 
Documentation Available Source Code FORTRAN - Available 
Pre Processor Available Post Processor Available 
Other Model Features Includes resuspension of silts and clay 
Other Capabilities Includes heat exchange and evapotranspiration modules 
The stream channel simulation includes flow routing and oxygen and nutrients biochemical modeling (through phytoplankton) 
Is able to simulate point and non-point sources, is integrated into the EPA BASINS GIS based modeling support system 
Limitations Assumes that the receiving water body is well-mixed 

Model Evaluation Sheet 
Model No. 28: RCA 
Component A: Hydrodynamics 
Dimension Spatial: Coupled with ECOMSED or EFDC Time: Unsteady 
Model Characteristics WQ model that has been applied to rivers, lakes, estuaries and coastal systems 
Wetting and Drying Depends on the hydrodynamic model used Ground Water Flow Depends on the hydrodynamic 
model used 
Additional Information Uses finite difference 
Component B: Water Quality 
Components Simple and advanced eutrophication, wetland systems 
Vegetation Algae (multiple algal groups) 
Soil Includes a sediment nutrient flux subroutine (deposition and resuspension) 
Additional Information Fully closed P and N cycles, complete DO/BOD dynamics 
The model is based on USEPA WASP 
Component C: General 
Public Availability Available Contact Information HydroQual, Inc.; Hydroqual.com 
Run Time No information Platform UNIX, LINUX and Windows 
Acceptance New Model Technical Support No information 
Documentation Partial Source Code Available, FORTRAN 
Pre Processor No information Post Processor No information 
Other Model Features Flexible input structure (different points and diffuse sources) 
Other Capabilities Transport of dissolved and particulate substances 
Includes volatilization in the water-air interface 
Limitations The model was recently release for public use; it has not been fully tested 

Model Evaluation Sheet 
Model No. 29: GLEAMS (Groundwater Loading Effects of Agricultural Management Systems) 
Component A: Hydrodynamics 
Dimension Spatial: Field Scale Time: Daily variations 
Model Characteristics The models simulates runoff and percolation 
Wetting and Drying Partial Ground Water Flow Percolation-vertical movement 
Additional Information It consists of four major components: hydrology, erosion/sediment yield, pesticide transport, and nutrients 
The model tracks movement of pesticides with percolated water, runoff, and sediment 
Component B: Water Quality 
Components Conservative, erosion and sediments, pesticides, nutrients 
Vegetation Plant uptake of pesticide 
Soil Soil profile description and crop data are used to estimate effective rooting depth 
Additional Information Soils data are input by soil horizon, and the model distributes values of porosity, water retention characteristics, and organic matter 
into the appropriate computational layers 
Component C: General 
Public Availability Available Contact 
Information 
Daren Harmel, USDA-ARS, Temple, TX 
http://www.cpes.peachnet.edu/sewrl/Gleams/gleams_y2k_update.htm 
Run Time Computationally Efficient -FAST Platform Windows 
Acceptance Wide Technical Support No longer supported by ARS 
Documentation Available - Complete Source Code FORTRAN 
Pre Processor Available in C code Post Processor Included 
Other Model Features Upward movement of pesticides and plant uptake are simulated with evaporation and transpiration 
Other Capabilities Widely used to simulate nutrient nonpoint source impacts on water quality, nutrient dynamics may be incorporated into RSM 
Nutrient dynamic formulation may provide ideas for implementation in other models 
Limitations Assumes that a field has homogeneous land use, soils and precipitation 
Field scale model 

Model Evaluation Sheet 
Model No. 30: BLTM (Branched Lagrangian Transport Model) 
Component A: Hydrodynamics 
Dimension Spatial: 1D with branches Time: Dynamic 
Model Characteristics Must be integrated with flow model (BRANCH and DAFLOW frequently used) 
Wetting and Drying It is not included Ground Water Flow It is not included 
Additional Information The model solves the one-dimensional convective-diffusion equation with reaction kinetics 
Component B: Water Quality 
Components Two subroutines are available, one to route any number of independent constituents with first order decay, and one which duplicates 
the reactions kinetics in the EPA QUAL2E 
Vegetation Phytoplankton 
Soil 
Additional Information The model includes a subroutine to predict stream temperature 
Component C: General 
Public Availability Available Contact 
Information 
Harvey E. Jobson, USGS 
http://water.usgs.gov/software/bltm.html 
Run Time No information Platform Windows, UNIX 
Acceptance Wide Technical Support No information 
Documentation Available - Complete Source Code FORTRAN 77 
Pre Processor Included Post Processor Included 
Other Model Features Specalized reaction kinetics can be easily developed by modifications to one of the existing kinetic subroutines 
Other Capabilities Water quality model, easily modified by user. Lagrangian technique eliminates numerical dispersion 
Limitations 

Model Evaluation Sheet 
Model 31: SWAT (Soil and Water Assessment Tool) 
Component A: Hydrodynamics 
Dimension Spatial: Lumped 2D, Field Scale Time: Daily variations 
Model Characteristics The model includes surface runoff, base flow, transmission losses, pond and reservoir storage, reach routing and groundwater flow 
Wetting and Drying Partial Ground Water Flow Included 
Additional Information Surface runoff volume is computed using a modification of the SCS curve number method or the Green @ Ampt infiltration method 
SWAT partitions groundwater into a shallow, unconfined aquifer and a deep-confined aquifer. Open channel flow is calculated using Manning’s equation 
Component B: Water Quality 
Components Nitrogen and phosphorus cycling. Nutrients routing. Algae, DO and BOD models 
Vegetation Plant growth model. Nutrients plant uptake is simulated 
Soil Includes transformation of N and P in the soil. In addition to plant use, the nutrients may be removed via mass flow of water 
Additional Information SWAT tracks the movement and transformation of several forms of N and P in the watershed, and nutrient transformations in the 
stream are controlled by the in-stream WQ model which is adapted from QUAL2E 
Component C: General 
Public Availability Available Contact Information www.brc.tamus.edu/swat/ 
Jeff Arnold; jgarnold@spa.ars.usda.gov 
Run Time Computationally efficient Platform DOS/Windows, UNIX 
Acceptance Wide Technical Support No information 
Documentation Available Source Code Available 
Pre Processor Included Post Processor Included 
Other Model Features Incorporates features of SWRRB, CREAMS, GLEAMS and EPIC. The model includes a SWAT/ArcView interface 
Other Capabilities Enable users to study long-term impacts, e.g., several decades. 
In addition to return flow, water stored in the shallow aquifer may replenish moisture in the soil profile in dry conditions 
Model components also include weather, percolation, ET, crop growth, irrigation and water transfer from channels and reservoirs 
Limitations SWAT is a continuous time model, i.e. a long-term yield model. It is not designed to simulate detailed, single-event flood routing.