The largest Florida manatee (Trichechus manatus latirostris) aggregation at a natural warm-water refuge occurs in Kings Bay, Crystal River, FL. Over the last 32 years, the U.S. Fish and Wildlife Service and the State of Florida have created a network of manatee protection areas within Kings Bay including a year-round refuge designation and seven Federal manatee sanctuaries during the winter manatee season (November 15 – March 31). Aerial survey data collected between 1983 and 2012 was used to examine the seasonal change in manatee distribution within Kings Bay in order to assess the effectiveness of current sanctuary sizes and locations. Regression analysis indicated a significant change in manatee abundance among the winter seasons (p < 0.05). The average winter manatee counts increased by 4.81 animals per year over the 30 year period. In contrast, no significant changes in average or peak manatee abundance was detected among the summer seasons (p = 0.71 and p = 0.45 respectively). The average manatee counts increased by only 0.109 animals per year over the summer periods. Spatially explicit models using Geographic Information System (GIS) analysis revealed a strong correlation between high manatee density and artesian springs during the winter seasons. Highest abundances were identified at three locations: King’s Spring, Three Sisters Springs, and Magnolia Springs. These three locations coincide well with pre-existing sanctuary designations, but additional coverage is needed to support the overflow of manatees outside of sanctuary boundaries. Manatees continued to use Kings Bay in the summer seasons but in lower numbers and densities. Because density patterns were not uniform across summer periods, a heavier reliance on boat speed regulation is recommended to provide adequate protection to the endangered Florida manatee. Within a habitat type, the Magnolia Springs, South Banana Island, and Three Sisters Springs sanctuaries exhibited a significant influence on manatee density, suggesting differences in quality among sanctuaries. Years coinciding with extreme cold weather events also had a significant influence on manatee density. Using GIS to investigate seasonal shifts in manatees can be very informative regarding many issues including habitat selection and may improve the design and management of protected areas.

Optical parameters measured via absorption spectroscopy and high-resolution fluorescence spectroscopy were used to characterize dissolved organic matter (DOM) in the springshed of Kings Bay, a spring-fed estuary located on Florida's Springs Coast. Over the past 40 years, springs supplying groundwater to Kings Bay have shown an increase in nitrate concentration. The overall goal of this project was to fingerprint wells and spring sites with elevated nitrogen concentrations using CDOM optical properties and establish relationships between nutrient and optical parameters. Samples were obtained from various sites: springs, Kings Bay surface (KBS), wells, coastal waters in and at the mouth of Crystal River (Coast) and lakes and rivers (LNR), during dry and wet seasons. The relationships between the environmental parameters and traditional optical parameters which provide insight into source characteristics were analyzed. Excitation emission matrix spectroscopy (EEMS) provided information about the concentration and chemical nature of organic matter in the study area. CDOM optical properties combined with salinity clearly separated the sources of fixed nitrogen in the Bay. Northern springs with elevated dissolved inorganic nitrogen (DIN) concentration had lower salinities and showed a presence of protein peaks. CDOM concentration was negatively correlated with total nitrogen (TN) and DIN, which suggests that these are subjected to anthropogenic influences. Humic peaks dominated the composition of the southern springs. CDOM concentrations were much higher than in the northern springs and there was a positive correlation between CDOM and both TN and DIN. These findings suggest that the fixed nitrogen in the southern springs is naturally occurring organic matter and the low concentrations may partially be a result of subsurface mixing of saltwater and freshwater in the aquifer. Thus, hypothesis testing showed that there was a significant difference between northern and southern springs Hypothesis testing also showed that there is a significant and unexpected positive relationship between CDOM and salinity studying Kings Bay, which is due to the low CDOM concentration in the springs discharging fresh water. This unique dataset also determined that the intercept of the mixing line was significantly different form zero. This indicates that CDOM is present and detectable at very low concentrations. Parallel Factor Analysis (PARAFAC) was used to evaluate CDOM composition from excitation emission matrix spectra (EEMs) and five components were identified: two humic, two marine humic, and one protein-like. The marine-like components, peak M, were produced in the marine environment and in meteoric groundwater. The study found a unique groundwater marker for coastal regions. Northern Kings Bay sites were characterized by a protein-like component, which has been associated with wastewater. Additional optical and environmental parameters were used in discriminate analysis, which successfully identified the CDOM markers for both natural and anthropogenic sources of nutrients in the environment. It is vital to improve the analysis of water, nutrients, and carbon from groundwater discharge into the coastal zone. Elevated DIN concentrations in groundwater are a widespread problem in Florida and over the past 30 years many spring waters have shown an increase in DIN concentrations. Nutrient discharge into delicate coastal areas can lead to ecological concerns. Investigating CDOM and nutrient distribution together can be a beneficial tool that can help differentiate sources from riverine/lacustrine, estuarine, marine, groundwater, and sewage impacted categories.