Rookery Bay National Estuarine Research Reserve (RBNERR), located just south of Naples, Florida, has suffered from large fluctuations of freshwater inflow, which have had significant impacts on fish and invertebrate species within the estuary. Historically, Rookery Bay had freshwater inflows of 2,500 cubic feet per second per month (cfs/month) but during the early 1990’s, the inflows regularly exceeded 10,000 cfs/month. Maintaining salinity levels is crucial to conserving and protecting estuarine habitats of Rookery Bay. Currently, the Florida Department of Environmental Protection, the Florida Fish and Wildlife Conservation Commission, and the University of South Florida are joining efforts to determine optimal freshwater inflow from the weir upstream, which regulates the freshwater entering the estuary. Habitat suitability modeling (HSM) using Geographic Information Systems (GIS) will be used to predict seasonal spatial distributions and relative abundance of estuarine species by life stage across Rookery Bay. Physical parameters such as salinity, dissolved oxygen, bottom type, temperature, and depth will be interpolated across the estuary using ArcGIS Spatial Analyst. These physical parameters will be the habitat layers associated with the model and the habitat affinities for key species will be consequential from indices derived from previous HSM in Charlotte Harbor (nearby estuary). Salinity, dissolved oxygen, temperature, and depth are all parameters of the estuary that are partly dependent upon atmospheric and surface variables. The project involves obtaining 12 years of meteorological and climatological data from the South Florida Water Management District. The various weather stations within the watershed will provide the means to assemble seasonal composites of rainfall and temperature interpolated across the watershed by season. The resulting GRIDS will be used to acquire insight on seasonal temperature and rainfall variations from 1990 to 2002 and determine the rolls they play on the condition of the estuary. Data loggers located in the upper and lower estuary have historically recorded estuarine conditions since 1990. Data will be used to verify that air temperature and rainfall are important in determining estuarine characteristics, which in return effect the fish and invertebrate species. The results of this preliminary study will provide water managers of the South Florida Water Management District further insight on the regulation of water through the weir (based on seasonal variation) which controls the amount of freshwater entering the estuary. The study will also provide water managers further insight on optimal estuarine conditions from the HSM models as well as a synopsis of estuarine conditions with relation to historical climatological conditions.