We evaluated nekton habitat quality at 5 shallow-water sites in 2 Rhode Island systems by comparing nekton densities and biomass, number of species, prey availability and feeding, and abundance of winter flounderPseudopleuronectes americanus. Nekton density and biomass were compared with a 1.75-m2 drop ring at 3 sites (marsh, intertidal, and subtidal) in Coggeshall Cove in Narragansett Bay and two subtidal sites (eelgrass and macroalgae) in Ninigret Pond, a coastal lagoon. We collected benthic core samples and examined nekton stomach contents in Coggeshall Cove. We identified 16 species of fish, 16 species of crabs, and 3 species of shrimp in our drop ring samples. A multivariate analysis of variance indicated differences in total nekton, invertebrates, fish, and winter flounder across the five sites. Relative abundance of benthic invertebrate taxa did not match relative abundance of prey taxa identified in the stomachs. Nonmetric multidimensional scaling plots showed groupings in nekton and benthic invertebrate prey assemblages among subtidal, intertidal, and marsh sites in Coggeshall Cove. Stepwise multiple regression indicated that biomass of macroalgae was the most important variable predicting abundance of nekton in Coggeshall Cove, followed by elevation and depth. In Rhode Island systems that do not experience chronic hypoxia, macroalgae adds structure to unvegetated areas and provides refuge for small nekton. All sites sampled were characterized by high abundance and diversity of nekton pointing to the importance of shallow inshore areas for production of fishes and decapods. Measurements of habitat quality should include assessment of the functional significance of a habitat (this can be done by comparing nekton numbers and biomass), some measure of habitat diversity, and a consideration of how habitat quality varies in time and space.