To gauge the influence of salinity on the habitat value of oyster reefs, spatial and seasonal patterns of the presence of reef-resident fishes and decapods were assessed in the Caloosahatchee, Estero, and Faka-Union estuaries of Southwest Florida. Lift nets (1 m²) containing 5 L of oyster clusters were deployed on intertidal reefs at three sites along the salinity gradient of each estuary. Nets were deployed during three seasonally dry and three seasonally wet months for a period of 30 d. Oyster densities were estimated at each site and a number of community metrics were calculated as a measure of habitat use (e.g., organism density, biomass, diversity, dominance, richness). Several metrics increased downstream in one or more systems (e.g., organism density, biomass, diversity) and in general appeared to be more related to salinity than to the density of living oysters present. Although organism density was higher during the wet season for all three systems, biomass was higher during the dry season in the Caloosahatchee. In the Caloosahatchee and the Estero, measures of biodiversity tended to be higher during the dry season. These results suggest that the salinity requirements of the organisms that inhabit oyster reefs should be considered in the planning of oyster-reef restoration or enhancement projects or in the management or alteration of freshwater inflow into estuaries.