Nekton communities in northeastern Florida Bay have been affected by long-term alterations in water delivery and area closures to protect the American Crocodile. Currently, projects are underway to restore freshwater inflow to Florida Bay, and closed areas are being reopened to the public to allow for more recreational fishing opportunities within Everglades National Park. To address the effects of recent changes, nekton community metrics and recreational fisheries across three hydrologically-distinct basins of varying public access (Little Madeira Bay ‒ closed since 1980, Joe Bay ‒ recently reopened, and Long Sound ‒ open) were compared across seasons (wet vs. dry) and water years (2016-2019) using fisheries-independent surveys with seines and baited remote underwater video (BRUVs). Patterns in catch-per-unit-effort and species richness were consistent among gear types, with higher abundance and richness observed in Little Madeira and Long Sound relative to Joe Bay for small- and large-bodied nekton. Inherent basin differences related to hydrology, water depth, substrate, and submerged aquatic vegetation were more important in structuring the nekton communities than public access, and benefits to recreational fisheries were only observed in Little Madeira Bay. No temporal changes in the nekton communities or recreationally targeted species of Joe Bay were detected since its opening to public access. Instead, any temporal differences in the nekton assemblages within each basin reflected seasonal shifts or short-lived changes associated with Hurricane Irma (2017). Although BRUVs and seines revealed the same general patterns of species richness and abundance, the seine surveys were able to capture more of the species diversity, while the BRUVs were able to sample a greater variety of habitats. Therefore, for future monitoring of nekton communities in northeastern Florida Bay, we recommend the use of seine surveys since methods are standardized across the state of Florida, with BRUV surveys used in habitats inaccessible to seining.