The Guana Tolomato Matanzas National Estuarine Research Reserve (GTMNERR), located in Northeast Florida, serves as an ideal estuarine habitat for many economically and ecologically important species of fish and crabs. As climate change affects Florida ecosystems, the replacement of Spartina alterniflora (Smooth Cordgrass) marshes by northward-moving mangroves is possible. A change in the dominant vegetation has the potential to alter organic carbon inputs, which can lead to a shift in the primary and secondary consumers in the area. An assessment of the fish community is needed in the systems where the change from Smooth Cordgrass to mangrove is the most likely in order to determine which species and which breeding populations will be affected. We conducted a biodiversity survey over the course of 24 months to document the seasonal and spatial patterns in species richness, seasonal abundance, and size of species caught. From May 2013 to April 2015, we used a 15.24-m seine net to sample 8 sites within the GTMNERR. Comparable to many other estuaries, the catch per unit effort and species richness decreased in the colder winter months and rose through spring and summer. Temperature was the main factor that controlled the species assemblage, with some species recorded only during certain months of the year, while salinity was a minor parameter. Certain species were correlated with colder seasons, i.e., Leiostomus xanthurus (Spot) juveniles and Menidia spp. (silverside), or negatively correlated with other species, i.e., Spot and Fundulus similis (Longnose Killifish). Temperature and species interactions can be useful in tracking specific populations and the effects of anthropogenic influences in this system.