Estuaries are home to diverse, abundant fish communities. As increasing coastal development, habitat alteration and loss, and changes in water quality potentially impact fish biomass and biodiversity within estuaries, it is important to monitor for and understand changes in these important parameters, particularly as they relate to water quality. This study examined the relationships between fish catch per unit effort, fish biodiversity, and water-quality parameters—specifically phytoplankton biomass, phytoplankton biodiversity, and nutrient concentrations—from 2014 to 2016 within a lagoonal northeast Florida estuary. For this region, this is the first reported examination of the relationships between fish biodiversity, fish catch, and water quality that includes phytoplankton biomass and nutrients. We carried out monthly fish seine-net sampling, phytoplankton net tows, and water-quality sampling at 4 sites within the Guana–Tolomato–Matanzas estuary. Sites closer to Matanzas Inlet had lower fish biodiversity and higher fish catch per unit effort. Fish catch per unit effort and fish biodiversity showed a large degree of temporal variation and showed correlations with temperature, chlorophyll-a, and phytoplankton biodiversity. We examined differences between sites among fish communities in terms of water-residence time, phytoplankton biomass, and nutrient concentrations. The correlations of fish community biodiversity and CPUE with temperature, chlorophyll-a, and phytoplankton biodiversity, while important, likely represent only a subset of all the drivers regarding environmental conditions, habitat, prey, and predation, all of which influence fish community composition.