Assessments of how the fish assemblage in the Savannah River Estuary (SRE) might be affected from a proposed harbor expansion and deepening project for the Port of Savannah, Georgia, were hindered by the lack of information about the temporal and spatial distribution of fishes in the estuary. Accordingly, we conducted a year-long investigation to determine the temporal and spatial distribution of estuarine-dependent fishes along marsh edges and in tidal creeks of the SRE. We used various seines to sample the fishes monthly at eight, 2-km long reaches of the SRE. During the fish sampling, we also measured temperature, salinity, dissolved oxygen, conductivity, and pH just below the surface (<1m) at sample sites. We used two-way ANOVA to evaluate species density and richness among seasons (spring, summer, fall, and winter) and habitats (polyhaline >15‰; mesohaline 5-15‰; oligohaline 1-5‰; and tidal freshwater <1‰). Fish sampling yielded 74 species and 21,739 individuals. Fish density and richness varied either among habitats or seasonally (p <0.01). Fish density and species richness were low in fall, increased in late winter, and peaked in spring. Spatial patterns in fish distribution were less recognizable. Most members of the fish community were estuarine generalists capable of tolerating a wide range of salinities (5.0‰-15.0‰). Marine species whose distribution was limited to areas with higher salinities (>10‰) comprised a smaller subset of the assemblage. These species occasionally invaded the estuary as the salt wedge moved inland during periods of low river discharge. Obligate freshwater species and those intolerant of salinities above 5.0‰ were a small component of the assemblage. Members of this latter group may be at the greatest risk of range contraction or population declines in the advent of increased salinities in the estuary, which would be expected if the harbor were deepened.