We examined the community structure of fish and selected decapod crustaceans and tested for within estuary differences among habitats at depths of 0.6 m to 7.9 m, in Great Bay and Little Egg Harbor in southern New Jersey. Several habitat types were identified a priori (e.g., eelgrass, sea lettuce, and marsh creeks) and sampled by trawl (4.9 m headrope, 19-mm mesh wings, 6.3-mm mesh liner), monthly, from June 1988 through October 1989. Repetitive (n=4) 2-min trawl tows were taken at each habitat type from 13 locations. The fishes and decapod crustaceans collected were typical of other Mid-Atlantic Bight estuaries but varied greatly inseasonal abundance and species. In the years sampled, bay anchovy (Anchoa mitchilli) was the dominant species (50.5% of the total number), followed by spot (Leiostomus xanthurus) (10.7%), Atlantic silverside (Menidia menidia) (9.7%), fourspine stickleback (Apeltes quadracus) (5.9%), blue crab (Callinectes sapidus) (4.6%), and northern pipefish (Syngnathus fuscus) (4.2%). The biota were examined by multi-dimensional scaling (MDS) for habitat associations and “best abiotic predictor” of community structure. Percent silt combined with salinity was the most important abiotic determinant of the faunal distributions among habitats. Temperature was a major factor influencing seasonal occurrence of the biota but had less effect on habitat comparisons. The analysis confirmed the distinct nature of the assemblages associated with the habitats, that is, eelgrass, upper estuary subtidal creeks, channels, and open bay areas. Several species were associated with specific habitats: for example,A. quadracus andS. fuscus with eelgrass, clupeids with subtidal creek stations,L. xanthurus with marsh channels, and black sea bass (Centropristis striata) and spotted hake (Urophycis regia) with sponge-peat habitat. Species richness appeared to be positively related to habitat structural heterogeneity. Thus, the best predictors for these estuarine fish and decapod crustacean assemblages were seasonal temperature, percent silt and salinity combined, and the physical heterogeneity of the habitat.