The work of this Master of Science thesis project is an analysis of salinity effects on nearshore epifauna along the western shore of Biscayne Bay in southeast Florida, USA. Field collection surveys have found a high probability of occurrence of bigeye mojarra (Eucinostomus havana) in salinities near 25 ppt. In a salinity gradient observation experiment test subjects of the same species and size class were also observed more frequently at 24 ppt. In this analysis presence and abundance patterns found in field surveys were compared with behavioral results obtained in the observation tank. This apparatus provided insight into distribution patterns of the bigeye mojarra (Eucinostomus havana) and possible changes in distribution that may result from habitat changes in the future. Historically, the western shore of Biscayne Bay was more freshwater marsh than the mangrove dominated marine environment that prevails today. Changes to fresh water inputs into the Bay are planned through projects of the Comprehensive Everglades Restoration Plan (CERP). CERP is a joint Florida state and U.S. federal effort to redesign surface water flow through the canal system of South Florida, replenish the Everglades ecosystem, and restore a more natural quantity, timing, and distribution of flow into Biscayne and Florida Bays. Approved by the U.S. Congress as part of the Water Resources Development Act of 2000, CERP will be implemented by the South Florida Water Management District (SFWMD) and the U.S. Army Corps of Engineers (USACE). This plan is designed to restore the ecosystem from its freshwater core to the coastal wetlands recreating a condition close to that existing before the current system of flood control drainage canals was begun in 1903 and continued by the federal Central and Southern Florida Project in 1948 (www.evergladesplan.org). Changes are planned to divert a portion of canal flows to Biscayne Bay into coastal wetlands as sheet flow and surface runoff. Planned changes to freshwater delivery may change the habitat along the shoreline and thus the distribution of prey organisms living in this habitat. This may in turn affect predator fish important to local recreational and commercial fisheries as well as other predators such as wading birds. The analysis and prediction provided in this thesis work is important for better understanding the effects of restoration efforts on the Bay nearshore habitat and its condition as essential fish habitat, which is federally regulated by the Magnuson-Stevens Fishery Conservation and Management Act (Magnuson-Stevens, 1996). The distribution of small fish and invertebrate inhabitants of the nearshore environment and habitat environmental qualities have been recorded over the past five years from throw-trap surveys of the western shoreline of Biscayne Bay as part of a CERP-sponsored monitoring program. This pattern is correlated with salinity, but there may be other factors affecting the distribution of this species.

The purpose of this thesis is to determine the factors that contributed to the decline of Florida apple snail ( Pomacea paludosa) populations in the A.R.M. Loxahatchee National Wildlife Refuge with the goal of devising management recommendations to the Refuge regarding population management strategies. The factors examined that could have potentially contributed to population decline include the use of copper-based herbicides, insecticide application, the occurrence of drought, the use of other herbicides, the occurrence of fire, and non-avian predation. Annual Narrative documents produced by Refuge managers and staff members, dated from 1951 to 2007, were used to collect historical data for these factors. The quality of data reporting within the Annual Narratives was also examined. To support data on droughts documented in the Annual Narratives, surface water and rainfall data were obtained and analyzed. The methodology includes the use of conceptual ecological models and historical ecology to determine whether or not the factors examined produced an ecological effect capable of affecting the Refuge population of apple snails. Evidence from the Annual Narratives suggests that the use of copper-based herbicides, the occurrence of drought, and predation by alligators were responsible for the decline of the apple snail on the Refuge. A lack of consistently reported data regarding apple snail densities makes it difficult to determine the degree to which each factor had an effect on the apple snails or to determine if any spatio-temporal relationship existed between the Florida apple snail and Everglade snail kite ( Rostrhamus sociabilis plumbeus) based on copper-based herbicide use. The overall quality of the Annual Narratives improved throughout the study period and eventually focused heavily on investigative studies. Several management recommendations were suggested to improve Florida apple snail populations on the Refuge. First, in order to monitor the health and trends of the apple snail population, a monitoring network needs to be established with results maintained in a geodatabase. Both apple snail density and egg cluster counts need to be made following an established sampling method. Second, in an attempt to sustain higher apple snail densities, stocking of the interior should be attempted. Finall, in the event that adjacent farmlands are to be restored, soil samples need to be analyzed to determine if concentrations are high enough that desorption of copper from the flooded agricultural soils could pose a serious threat to the Refuge by reintroducing toxic levels of copper.

The Florida Everglades presents a model setting for studying animal-habitat relationships in a dynamic landscape that is heavily influenced by seasonal hydrology and water management. I used dynamic, high-resolution habitat classification maps and radio-telemetry to examine habitat preference of Largemouth Bass, Bowfin, and Florida Gar before and after a field-scale manipulation was established to address uncertainties with Everglades restoration and water management practices. Results indicate preference for the canal habitat by all three species, which represents only a small portion of the submerged landscape even in the driest conditions. Bowfin and Florida Gar were more likely to be relocated within marsh habitats than Largemouth Bass. Preference for the canal habitat increased after landscape alteration and was influenced by water management practices rather than hydrological or environmental factors. Partial canal backfilling may assist with accomplishing restoration goals while maintaining preferred habitat for economically and ecologically valuable predatory fishes.

The Florida Everglades is a massive and highly managed subtropical wetland ecosystem, strongly influenced by anthropogenic control of freshwater distribution and highly susceptible to a changing climate, including rising sea-level and changes in temperature and rainfall. Shifting hydrologic regimes impact ecosystem function and biogeochemistry, which in turn control the sources, fate, and transport of organic matter. As a master environmental variable, it is essential to understand how organic matter dynamics will respond to changes in the balance between freshwater and saltwater associated with landscape-scale Everglades restoration efforts and climate change. The research comprising this dissertation improves current understanding of the linkages between organic matter and hydrology in the Everglades across a broad range of temporal and spatial scales. A range of research tools, including stable molecular biomarkers, water quality sensors, data synthesis and multivariate statistics were utilized. Biomarkers were used to track particulate organic matter mobilization in response to experimentally manipulated flows and provided initial evidence that sheet flow restoration can re-engineer landscape microtopography, influencing both ecosystem structure and organic matter inputs to Everglades National Park (ENP). Short-term and long-term temporal studies indicated the quantity and quality of dissolved organic carbon responds to changes in freshwater flow to marshes and mangrove forests in ENP, and that spatial patterns and trends are driven by a complex mixture of managed and natural surface water inputs (i.e., rainfall and water management inflows) as well as groundwater discharge. Application of climate scenario forecasting to relationships established between organic matter and hydrologic drivers predicted reductions in dissolved organic carbon export from ENP and changes in organic matter molecular composition. Furthermore, high-frequency measurements showed hydrologic connectivity of freshwater and estuarine organic matter pools at sub-monthly time-scales. In summary, the work presented here clearly indicates strong yet spatiotemporally complex relationships between changes in water and the sources and transport of organic carbon through the Everglades.

The Florida Everglades ecosystem is threatened by human development, increased pollution, freshwater scarcity, and invasive species; factors that have negatively impacted the Everglades and native species health and populations. Man-made canals and levies have redirected the natural flow of fresh water from Lake Okeechobee into the Florida Everglades, starving central and south Florida ecosystems of necessary fresh water and nutrients. Through the efforts of the Comprehensive Everglades Restoration Project (CERP), freshwater is being redirected back into central and south Florida, returning the sheet flow of water back into the Everglades. Monitoring species abundance in the Everglades is a beneficial conservational tool for assessing restoration efforts from CERP. As a semi-aquatic apex predator, river otters (Lontra canadensis) are a useful health bio-indicator for the Florida Everglades. In order to conduct future population studies of river otters in the Florida Everglades, it must first be ascertained where they can be found and what time of year they are most likely to be sighted. For this study, Moultrie infrared game cameras were used to photograph the presence or absence of river otters within the five main habitats in the Everglades; the pinelands, hardwood hammock, cypress swamp, marsh prairie, and mangrove estuary at two protected areas in the Florida Everglades (Big Cypress National Preserve and Fakahatchee Strand State Park). River otters were most frequently sighted in the hardwood hammock habitat, but were also found in the cypress swamp. The large majority of river otter sightings occurred during dry season, which is thought to be a function of restricted water availability and aquatic mobility. Future population studies of river otters would be most productive in the hardwood hammock and cypress swamp habitats during dry season. Game camera images along with field opportunistic sightings, resulted in a variety of species documented. This provided valuable information of species richness and distribution within and amongst the habitats. The hardwood hammock was found to be the most species rich habitat, having over half the species observed in the study in this habitat. The Aves class was the most abundantly observed in the Everglades, and was most frequently sighted during the dry season. As a refuge for migratory birds, the Everglades house the majority of bird species during the winter months, which occur during dry season. The Aves class was most frequently sighted in the pinelands habitat during dry season. This habitat, being the highest in elevation and therefore the driest, shows a stronger resemblance to most northern bird habitats then does the water-saturated wetlands found throughout the Everglades. The mangrove estuary was the most commonly occurring outlier, having the least species overlap when compared to the other habitats. All other habitats in the Everglades are freshwater wetlands, while the mangrove estuary is a brackish environment, which limits the species that are unable to tolerate saline conditions. Further studies of species abundance throughout the Everglades will aid in monitoring CERP restoration efforts over time.