Lower West Coast

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PROJECTS Southwest Florida Feasibility Study C-43 Basin Storage Reservoir Picayune Strand Hydrologic Restoration Henderson Creek/Belle Meade Restoration

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Overview

Florida lies beyond the range of most CERP projects and models. The C&SF Project Comprehensive Review Study recommended a feasibility study to identify southwest Florida water resource conditions and to develop potential solutions to any problems that might be identified. DOI has a great interest in this area, which covers approximately 4,300 square miles and includes two major drainage basins and the largest subtropical mangrove estuarine ecosystem in the United States. Lands under DOI stewardship include the J.N. "Ding" Darling and Florida Panther /Ten Thousand Islands National Wildlife Refuges, Big Cypress National Preserve, and Everglades National Park.

Drainage to support intensive urbanization has significantly decreased coastal wetlands and altered the freshwater inflows and salinity in the southwest coastal estuaries and bays. A principal goal for all of the southwest Florida hydrologic restoration projects is the reestablishment of natural freshwater flows and salinity in these areas. The Henderson Creek/Belle Meade Restoration Project and the Picayune Strand Hydrologic Restoration Project are similar projects that propose to meet this goal through a combination of rehydrating wetlands, removing barriers to sheetflow, and reducing canal point discharges.

Because the 2 x 2 Model does not have a database that includes southwest Florida, the SFWMD has created a regional hydrologic model, the MIKE-SHE, to fill this gap, and it is being used to predict how water will change under different alternatives. A fully verified regional physical model needs to be developed and integrated with ecological models to more accurately predict salinity patterns and the responses of biological communities and species to hydrologic changes.

Landscape level restoration in southwest Florida may require decisions that favor one species or trophic level over another or that maximize biodiversity within an ecological system. Assessment tools to support this level of decision making are a critical priority of long-term regional resource planning. Species of particular concern in southwest Florida include such far-ranging species as the Florida panther, West Indian manatee, wood stork, and migratory birds.

DOI managers can most effectively participate in CERP projects during three project stages: (1) NEPA scoping in the early stages of project design, to help ensure that hydrologic targets accurately reflect the natural pre drainage conditions, (2) review of project alternatives, to ensure that fish and wildlife and parks are adequately considered in compliance with DOI mandates, and (3) monitoring and assessment of project results, to support project modification if needed to ensure that the intended conditions are achieved. The major questions that DOI managers need to answer at each stage to effectively fulfill their responsibilities as partner and steward are summarized below, along with the highest priority science needs for answering those questions. This information is discussed in greater detail for each individual project following this summary.

SUMMARY OF DOI SCIENCE NEEDS RELATED TO THE LOWER WEST COAST

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Southwest Florida Feasibility Study

Project Purpose and Major DOI Interest

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The C&SF Project Comprehensive Review Study recommended a feasibility study to identify southwest Florida water resource conditions and to develop potential solutions to any problems that may be identified. Although most of southwest Florida lies outside the area covered by the CERP models, it is known that dredging, filling, and channelization have altered the hydrology of this region, resulting in significant adverse effects on native habitats and wildlife. Lee County alone has lost 19% of its original mangrove forests.

The project area includes the Caloosahatchee and Big Cypress watersheds. Historically, the Caloosahatchee River was a shallow, meandering 50-mile-long drainage. This watershed includes a pristine mangrove-dominated estuary, a habitat unique in the continental United States. Mangroves support fish and macroinvertebrate communities by providing protected nursery areas and food for a multitude of important commercial and recreational marine species.

As a result of dredging and channelization beginning in 1884, the river now extends 71 miles from Lake Okeechobee to San Carlos Bay. The river is managed by three locks, the most downstream of which also serves as a barrier to salinity and tide within the 26-mile-long estuarine portion of the Caloosahatchee River. Water releases from Lake Okeechobee occur through a series of locks when lake levels exceed the USACE criteria for flood protection.

The Big Cypress watershed of the region drains to the coastal marshes and mangrove swamps of Estero Bay, Rookery Bay, and the Ten Thousand Islands. This area includes extensive urban and agricultural development as well as public land holdings and has historically been one of the most rapidly developing areas in the nation. There are a significant number of canals and structures in the watershed, the operation of which affect interior wetlands and receiving waters.

The Southwest Florida Feasibility Study will address the health of upland and aquatic ecosystems in this 4,300 square mile area and consider a variety of parameters, including water flow, water quality, water supply, maintenance of existing flood protection, wildlife, biological diversity, and natural habitat. Given the large amount of public land in the study area, a major goal is to define the hydrologic linkages among nearly 30 federal, state, or county-managed areas and to coordinate the management and stewardship of these areas. DOI needs to continue its technical support role with the USACE through alternative development and subsequent project design and implementation.

The study area contains a number of wetland communities of significant concern to DOI, particularly short-hydroperiod freshwater marshes and wet prairies, seagrass beds, and mangrove forests. Up to 20 federally listed species and their critical habitat or experimental populations may occur within the study area. Southwest Florida likely represents the most important region of Florida in supporting wide-ranging listed species, such as the Florida panther, Florida black bear, and wood stork. Okaloacoochee Slough encompasses approximately 140,000 acres of primary habitat for Florida panthers. Area wetlands support the nation's largest historical wood stork rookery, the remnant of which is protected in Audubon's Corkscrew Swamp Sanctuary. Forty-three species of migratory nongame birds of management concern are supported by the southwest Florida ecosystem. Seagrass beds off the southwest Florida coast provide habitat and nursery grounds for many fish and invertebrate communities and are especially important in benthic-based primary productivity. West Indian manatees, waterfowl, fish, and wading birds rely heavily on seagrass systems as forage areas.

What Is Known
Studies have been completed on the function of ephemeral wetlands (seasonal ponds, freshwater marshes, isolated wet prairies, and hydric flatwoods) to establish those environmental characteristics critical to the survival and health of the numerous species adapted to the wet-dry annual seasonal regimes of South Florida. The wetland communities with the largest loss in the study area are short-hydroperiod freshwater marshes and wet prairies. Many species have life history cycles that are especially adapted to take advantage of the temporal nature of these habitats. These habitats also serve as seasonal refuges for species that are unable to survive or adapt to the altered hydrological cycles resulting from development. As water tables are lowered, the viability of these isolated ephemeral wetlands is reduced.

Background research and modeling, including a predevelopment vegetation map, a conceptual ecological model, and a regional simulation hydrological model (RSM), have been completed.

What Is Needed
Modeling to predict temporal and spatial variations in hydrologic conditions. Models that integrate sheetflow and groundwater conditions are needed to predict the temporal and spatial variations in hydrologic conditions that will occur with simulated depths of inundation in freshwater wetlands.

Modeling to predict temporal and spatial salinity patterns in estuaries. A principal goal for all of southwest Florida's hydrological restoration projects is the reestablishment of the minimum freshwater flows, and the elimination of freshwater point-source discharges, needed to restore more natural hydrology—and particularly salinity patterns—in estuaries. To have meaningful input into project targets, DOI managers will need to (1) understand how the hydrologic conditions in the estuaries are expected to change in response to hydrologic changes in the watershed and other restoration efforts, and (2) make assumptions about how the expected changes relate to the natural, predrainage hydrologic conditions in the estuary. The best tool for providing this information would be a fully calibrated and verified regional salinity model supported by continuous monitoring and other data acquisition.

This will require the development and calibration of estuarine mixing/circulation models. In order to predict the spatial and temporal salinity patterns in estuaries following upstream restoration, the dynamics of tidal and freshwater mixing must be understood. Hydrological modeling techniques now exist to allow development of these models. Once modeled, the effectiveness of estuarine restoration can be tested by comparing predicted salinity patterns with those empirically measured. Existing models such as the 2 x 2 Model and the NSM do not cover the feasibility study area. The hydrological model developed for the feasibility study area does not extend to the estuaries.

Modeling to predict trophic- or species-level responses to habitat changes. Development of evaluation tools to support landscape-level decision making is a critical priority for long-term regional resource planning. Ecological models needed for southwest Florida include (1) Florida panther response to habitat quality and quantity and changes in these habitats, (2) West Indian manatee response to changes in freshwater outflow and changes in seagrass distribution in estuaries due to watershed restoration activities, (3) migratory bird response to losses of forested ecosystems, and (4) wood stork response to alterations in wetland hydrology.

Identification and monitoring of key indicators. Research is needed to identify plant, invertebrate and vertebrate species that are diagnostic of particular hydrological conditions and that are responsive to hydrologic and water quality changes in the region.

C-43 Basin Storage Reservoir

Project Purpose and Major DOI Interest
The Caloosahatchee River once had an undistinguishable connection to Lake Okeechobee and probably received overflow from the lake only in abnormally wet years. The river was shallow and had numerous oxbows. Flooding was common. Water development activities, including the direct connection of the river through the C-43 canal to Lake Okeechobee, has highly altered the hydrology of the river and basin.

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The purpose of this project is to capture Caloosahatchee River Watershed (C-43 basin) runoff and releases from Lake Okeechobee. The reservoir will be designed for environmental, urban, and agricultural uses, water supply benefits, flood attenuation, and water quality benefits in terms of reduced salinity and nutrients in the Caloosahatchee Estuary.

Although WRDA 2000 did not specifically authorize construction of the C-43 Basin Storage Reservoir Project, WRDA authorized its inclusion in the development of a Project Implementation Report as part of the CERP.

This project is the first part of the C-43 Basin Storage Reservoir and ASR component. The project includes an aboveground reservoir with a total storage capacity of approximately 160,000 acre-feet located in the C-43 basin in Hendry, Glades, or Lee Counties. The initial design of the reservoir assumes 20,000 acres with water levels fluctuating up to 8 feet above grade. The final size, depth and configuration of this facility will be determined through more detailed planning and design. The C-43 reservoir will also be operated in conjunction with the Caloosahatchee Backpumping Project, which includes a stormwater treatment area for water quality treatment. If the level of water in the reservoir exceeds 6.5 feet and Lake Okeechobee is below a predetermined level, then water is released and sent to the backpumping facility. In order to restore the downstream estuaries, the proposed reservoir and STA must be located within the watershed.

The Caloosahatchee River basin contains both wetland habitats (freshwater swamps, sloughs, marshes, and estuaries) and upland habitats (pine flatwoods, temperate oak/palmetto hammocks, tropical hammocks, dry prairie, and xeric scrub communities). Although classified as distinct habitats, these systems form an interdependent mosaic, particularly for wide-ranging, imperiled species such as the bald eagle, Audubon's crested caracara, Everglade snail kite, and wood stork. The Caloosahatchee basin is also an important area for panther recovery. Also, a vital portion of the regional West Indian manatee population resides seasonally and/or year-round in the Caloosahatchee River and estuary.

The FWS is in the process of providing site and design recommendations to the USACE to reduce the direct and indirect impacts of the reservoir and STA on the habitat of threatened and endangered species in the project area. Even if large man-made reservoirs and STAs are sited in agricultural areas of relatively low habitat value, their long-term presence and operation in the Caloosahatchee watershed will modify the habitat quality for the four federally listed bird species (bald eagle, Audubon's crested caracara, Everglade snail kite, and wood stork) and perhaps other species, as well.

The flows from the Caloosahatchee River into the estuary directly affect the J. N. Ding Darling National Wildlife Refuge and also habitat on other public and private lands. A comprehensive conservation plan to comply with the National Wildlife Refuge System Improvement Act of 1997 is currently in preparation. The FWS is in the process of providing recommendations to reduce the direct and indirect impacts of this project on habitats throughout the watershed. As part of its analysis, the FWS will estimate the incidental take for all of the listed species when the preferred alternative is identified by the USACE.

What Is Known
A great deal of information on the manatee population in the Caloosahatchee River basin and the connecting C-43 basin has been collected and analyzed. Periodic surges of freshwater discharged into the Caloosahatchee River and its estuary during high rainfall events negatively impact the salinity level and habitat needs of the estuary. In addition to rapid salinity changes, these freshwater inflows affect nutrient loads and water transparency, which also control seagrass survival and distribution. Seagrasses support the estuarine food web and affect the distribution and movement patterns of manatees. The geographic distribution of food, warm-water refugia, freshwater sources, and the risk of boat-caused injury and mortality in the Caloosahatchee basin are factors that affect the recovery of the endangered manatee in this area.

What Is Needed
Modeling to determine natural flows in the Caloosahatchee River

Monitoring of bird species. Once sites are selected for these facilities, DOI will need to assess the type and degree of project impacts on federally protected species in the project area (bald eagle, Audubon's crested caracara, Everglade snail kite, and wood stork). DOI must use time and resources efficiently and quickly to collect and analyze baseline data and to synthesize it into recommendations that will assist the USACE in the design and construction of these facilities in ways that will minimize negative impacts on species and maximize potential benefits. After construction, habitat use at the facilities and in adjacent areas will be monitored, and the data analyzed to provide input into the adaptive management phase of the project. Indirect impacts related to the operation of the water management structures cannot be accurately predicted until operational plans are refined after construction and testing, at which time the FWS will need to reassess the indirect take these facilities will cause within the watershed.

Geographic information system (GIS) mapping for habitat database. The GIS-based tool the FWS has developed to map habitats for consideration in siting structures for the Lake Okeechobee Watershed Project will be refined and expanded with additional data for use in site selection that considers fish and wildlife values in the Caloosahatchee basin.⁶

Modeling and monitoring of West Indian manatee responses to habitat changes. DOI will use the current database and best available science to provide input to the USACE to reduce impacts on manatees. As more information is collected and analyzed, predictions of how manatee behavior will be affected by anticipated changes in their habitat will be linked to modeling and empirical studies of estuarine water circulation, salinity, water clarity, and seagrass distribution conducted by the SFWMD. Comparison of baseline data with post-construction conditions will be used in an adaptive assessment process to recommend changes in project operation or design to most benefit recovery of the manatee in this essential portion of its range. The operation of the water-storage and treatment facilities as an integrated system will be evaluated as part of an adaptive assessment program, and their effects on seagrasses and manatees will be part of this assessment.

Henderson Creek / Belle Meade Restoration

Project Purpose and Major DOI Interest
The Henderson Creek/Belle Meade Restoration Project is located about 5 miles south of Naples in southwestern Florida. The area known locally as the Belle Meade is the primary watershed for Henderson Creek, which drains into the Rookery Bay estuary. Collier County is currently facing unprecedented urban growth. Canals, roads, planned unit developments, commercial projects, and agriculture have greatly altered the volume, timing, and quality of freshwater entering the fragile estuarine ecosystems and severely restricted the ability of the associated wetlands to filter pollutants. While channelization and development have disrupted this system, acquisition and restoration of the undeveloped lands surrounding Henderson Creek, which link the watershed and estuary, can stop further hydrologic and habitat disturbance.

The primary DOI concern is to ensure that flows are managed to avoid unnatural surges of freshwater into one of the largest expanses of mangrove estuary in North America, part of which is protected inside the Ten Thousand Islands National Wildlife Refuge near Rookery Bay. The Rookery Bay National Estuarine Research Reserve and Ten Thousand Islands Aquatic Preserve, under the stewardship of the National Marine Fisheries Service and the Florida Department of Environmental Protection, are adjacent to the wildlife refuge. This region provides habitat for 14 federally listed threatened or endangered animal species, including the West Indian manatee. The bay also provides critical nursery habitat for commercially and recreationally important finfish and shellfish.

A weir situated north of Highway 41 is the main water control structure on Henderson Creek, controlling flows into Rookery Bay. Until recently, the weir could not be adjusted to mimic natural freshwater inflow patterns. Stream-gauging equipment was installed during the spring of 2001 to help regulate flow through the weir. The appropriate timing and amount of freshwater inflow through the weir on Henderson Creek need to be determined in order to conserve and protect listed species dependent upon the estuarine habitat in Rookery Bay.

What Is Known
Water circulation in Rookery Bay is a complex function of freshwater flows, tidal and wind forces, and local depths. Freshwater enters the bay through surface and groundwater flows and intense seasonal and episodic rains. Historically, surface freshwater percolated through wetland flowways before entering Henderson Creek and the bay.

Hydrologic manipulations and land use changes in the area over the past few decades have significantly affected the amount of freshwater entering Rookery Bay. Historically, the estuary received freshwater at about 2,500 cubic feet per second per month (cfs/month), but during the early 1990s the inflows regularly exceeded 10,000 cfs/month, a fourfold increase. Very high flows from Henderson Creek have occasionally resulted in rapid drops in salinity in the mid-region of the estuary, with significant impacts on water quality and biota.

What Is Needed
Additional analysis of Henderson Creek/Rookery Bay hydrology. Restoring this part of the ecosystem will require greater understanding of the spatial and temporal salinity patterns and the dynamics of tidal and freshwater mixing in the predrainage estuary and bay. To have meaningful input into project targets, DOI managers will need to (1) understand how the hydrologic conditions in the estuary will be expected to change in response to upland hydrologic changes and other restoration efforts, and (2) make assumptions about how the expected changes relate to the natural, predrainage hydrologic conditions in the estuary. The best tool for providing this information would be a fully verified regional physical model supported by continuous monitoring and other data acquisition. If it is not feasible to develop such a model before the project design phase, less sophisticated models can be used, and assumptions can be validated or refined during project assessment and adaptive management.

Four major tasks are necessary for this project: (1) understand the estuarine circulation patterns (and if possible determine salinity distribution under various freshwater inflow regimes), (2) gather temperature and salinity data across Rookery Bay and Henderson Creek associated with seasonal inflow regimes for four seasons, (3) map depths and bottom type within Rookery Bay using sonar, and (4) refine and validate information used to support decisions.

Research and possible model refinement to establish operating protocols

Modeling to predict the relative abundance and spatial distributions of estuarine fish and macroinvertebrates. Hydrologic and ecological model outputs will be needed to fully evaluate and predict the potential impacts of restoration alternatives. The Florida Fish and Wildlife Conservation Commission's Florida Marine Research Institute has been developing habitat suitability models that could be linked to the estuarine water circulation models. The modeling can be used to predict how changes in salinity/temperature patterns could influence the relative abundance and spatial distributions of important species of estuarine fish and macroinvertebrates.

Identification and monitoring of indicator species. Baseline information about the seasonal distribution of keystone species during both dry and wet seasons needs to be gathered and correlated with baseline hydrologic conditions. Modeling and verification of changes in species distribution as the project is implemented will improve the understanding of the linkages between potential freshwater inflow regimes from the Henderson Creek weir and the resulting ecological responses.

Picayune Strand Hydrologic Restoration

Project Purpose and Major DOI Interest
The Faka Union Canal System, completed in 1968, includes approximately 48 miles of canals intended to drain the proposed Southern Golden Gate Estates residential development project. The resulting hydrologic effect of these large canals is severe overdrainage of the area and large point-source freshwater discharges to downstream estuarine systems.

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The purpose of the project is to restore and enhance the fish and wildlife habitat, particularly wetlands, in Picayune Strand Hydrologic Restoration and on adjacent public lands by reducing overdrainage. A combination of spreader channels, canal plugs, road removal, and pump stations will reestablish more natural overland flows and improve the quality of the coastal estuaries by spreading the freshwater discharges more evenly among the bays and moderating the large salinity fluctuations currently caused by point discharges from the Faka Union Canal.

The project is located in the Big Cypress watershed of the Everglades region, in an area of approximately 94 square miles in southwestern Collier County. It is surrounded by a number of environmentally sensitive public lands, including the Florida Panther National Wildlife Refuge, the Ten Thousand Islands National Wildlife Refuge/National Estuarine Research Reserve/ Aquatic Preserve, the Belle Meade tract of the Picayune Strand State Forest, and the Fakahatchee Strand State Preserve. Changes in this region of the Everglades will also affect other parts of the Everglades, including Everglades National Park.

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What Is Known
It is estimated that the Faka Union Canal System has increased drainage by 16 times faster than historic conditions, lowered water tables by 2 to 4 feet, and reduced the hydroperiod by 2 to 4 months, resulting in a dramatic increase in forest fires and annual runoff. Wetlands in the project area have experienced significant historic losses through land use changes. Pine forest and freshwater marsh habitats have had the greatest losses in this area since 1900, with 88% of the pine forests and 59% of the freshwater marshes converted to other uses. The Southwest Florida Environmental Impact Statement indicates that an average of 508 acres per year of wetland fill was permitted in parts of Lee and Collier Counties from 1991 to 1998, and incremental losses are projected to continue. Remaining undeveloped areas are severely stressed by invasions of exotic vegetation, such as Brazilian pepper and melaleuca

The downstream estuarine systems are also adversely affected. Point-source freshwater discharges into Faka Union Bay are thought to be five times greater than those that historically occurred, while adjacent bays now receive less water. Four of the canals in this project flow into one major canal and then into Faka Union Bay, causing negative impacts to the estuary from freshwater pulses. Biological studies suggest that the canals have changed the salinity regime of the Faka Union Estuary, which has resulted in a reduction in submerged aquatic vegetation and a decrease in the estuary's value to fish and shellfish as nursery habitat. Species composition and standing stocks of submerged aquatic vegetation and macroalgae are sensitive to salinity variation. A comparison of information in several studies shows that seagrass cover in Faka Union Bay and other nearby bays has declined substantially since at least 1970. Oyster reefs, another critically important estuarine habitat, have been displaced seaward, where they are more subject to parasitic disease infestations.

What Is Needed
Refinement of the MIKE-SHE Model. Because this model will also be used to support the design of the project's structural components, it is important that it accurately predict the hydrologic conditions during local precipitation events. Further work will update topographic data, predict ground-surface water interactions, and develop reasonable precipitation amount/pattern assumptions for the project area.

Modeling to predict changes in hydrology and ecology in the Ten Thousand Islands NWR. A high-resolution hydrologic model is needed to predict the amounts, locations, and timing of flows through the Ten Thousand Islands refuge expected to result from this project. This model will be linked to a vegetation succession model to project ecological conditions and impacts on protected species and habitats under different water management regimes. Needed investigations will address the relationships between hydrology and factors such as fire, exotic plants, and aquatic prey species to determine how changes in hydrology will be expected to affect the distribution and viability of species such as wood storks, wading birds, and manatees.

Synthesis and study of the impacts of altered hydrology on the Florida Panther NWR. A study is needed to address how water levels have been altered and the affects of altered water levels and flows on terrestrial and freshwater wildlife habitats on the Florida Panther NWR, particularly how they have affected the spread of exotic plants, wading bird feeding and nesting success, and native plant communities.

Monitoring of water flows and water quality in receiving waters south of the project area. The extensive fresh and saltwater wetland habitats that exist south of U.S. 41 on the Ten Thousand Islands NWR and Fakahatchee Strand State Preserve are influenced by freshwater flows and water quality that have been altered by the Southern Golden Gate development project. A study to obtain baseline water flow and water quality data prior to Southern Golden Gate Estates restoration, and monitoring of water flows and water quality after the restoration, will determine what impacts the restoration has on water quality and quantity entering the wetland habitats south of U.S. 41.

Monitoring of effects on federally listed species affected by the project. Baseline, mid-project, and post-project studies will be conducted to monitor and determine the direct, indirect, and cumulative effects of this project on several federally listed species. Monitoring will cover three different habitat zones (estuarine, upland, and wetland) that provide habitat for the endangered species such as West Indian manatee, Florida panther, and wood stork. Baseline data and analysis will provide DOI with the most current information to aid in developing recommendations to the USACE on siting and design of the project components. Mid- and post- project monitoring will provide information on the effects of this project on the different habitat zones and the threatened and endangered species that inhabit them, as a basis for adaptive management of this project.

Monitoring of effects on wildlife within the Ten Thousand Islands NWR. A synoptic survey needs to be conducted of the current conditions of key habitats within the Ten Thousand Islands NWR, including hardwood hammocks, coastal islands, and emergent marsh. Key species including sea turtles, American crocodile, West Indian manatee, and water birds will be monitored to assess the effects of the project and guide adaptive management.

Monitoring of ecological responses to hydrologic change. State and federal agencies have begun baseline monitoring of fish and wildlife in the study area. This information will provide the basis for post-project analysis to determine if and to what extent hydrological restoration efforts benefit terrestrial and aquatic species. These studies need to be expanded to include larval sampling for amphibians, expanded sampling of aquatic invertebrates (including crayfish) and fishes, and standardized breeding bird survey protocols. Post-project vegetation studies will monitor wetland responses to hydrologic restoration efforts and provide information needed for adaptive management.

It is important that biological indicator studies be done to determine the effects of changes in freshwater flows on downstream estuarine communities and to verify the progress of coastal habitat restoration. These studies should include information on crab, oyster, fish, and marine invertebrate abundance and distribution in affected estuaries.

⁶ See the discussion of this topic for the Kissimmee basin, page 23.