Subtidal eastern oyster Crassostrea virginica (Gmelin) cover large expanses of many Gulf of Mexico estuaries; however, few researchers have attempted to quantify the value of deep, open-water, subtidal reefs as habitat for fishes and crustaceans as a result of gear limitations. We developed quantitative sampling gear for live oyster reefs by slightly modifying an epibenthic sled. Gear comparison trials showed similar effectiveness among marsh edge, submerged aquatic vegetation, and nonvegetated bottom for both epibenthic sled types. We then quantified the density and community assemblage of nekton and benthic crustaceans on deep subtidal oyster reefs in Lavaca Bay, TX, and compared it with densities found in nearby marsh edge, submerged aquatic vegetation, and nonvegetated bottom habitats. We found significantly fewer nektonic and benthic crustaceans on nonvegetated bottom and oyster reefs than in marsh edge and submerged aquatic vegetation over all seasons and regions, and community analysis revealed similar differences among habitat assemblages. Using gill nets, the greatest catch of transient fishes and crustaceans were collected on oyster reefs and nonvegetated bottom. Although relatively low densities of small juvenile fishes were observed over deep oyster reefs, our community analyses and the high catch-per-unit-effort of large, transient species provide evidence that subtidal reefs are a critical habitat for numerous estuarine fishes and crustaceans.