Monthly sampling was conducted during one year in three zones along the estuarine gradient of Baía de Vitória, Brazil. Within each zone, unreplicated night trawls were done in deep subtidal flats located 130–210 m away and 2–3 m deeper than shallow ones. Twenty-one taxa represented 97.5% of the total mean fish abundance. The taxa Achirus lineatus (mean±SD: 2076±1269 10−4 m2), Eucinostomus spp. (694±807), Symphurus tessellatus (400±626), Sphoeroides testudineus (367±597) and Lutjanus synagris (323±445) dominated the deep assemblage (N=36) while Eucinostomus spp. (3649±4913), A. lineatus (1287±1569), S. testudineus (1208±1986), L. synagris (1101±927) and Sphoeroides greeleyi (569±1404) dominated the shallow assemblage (N=35). Taxa exclusive of one or the other depth showed extremely low abundance. The low-salinity shallow flats showed higher total abundance and taxa number than the high salinity deep locales but richness, diversity and equitability showed no significant differences among the six stations. The assemblage structure was significantly correlated to the depth structure but not to physico-chemical characteristics of the water. However, the spatial distribution of individual species varied greatly, from depth-dependent pattern to estuarine gradient-dependent pattern, with several intermediates. The community structure is singular in comparison to that of other tropical Brazilian estuaries studied to date. This is probably related to its geographical position in a transitional zone between the northern, tropical Brazilian oceanic domain and the southern, subtropical-temperate domain.