In Grand Bay National Estuarine Research Reserve (Grand Bay NERR), Mississippi, we used quantitative drop sampling in three common shallow estuarine habitats— low profile oyster reef (oyster), vegetated marsh edge (VME), and nonvegetated bottom (NVB)— to address the dearth in research comparing nekton utilization of oyster relative to adjacent habitats. The three habitats were sampled at two distinct marsh complexes within Grand Bay NERR. We collected a total of 633 individual fishes representing 41 taxa in 22 families. The most diverse fish family was Gobiidae (seven species) followed by Blennidae and Poeciliidae (three species each). We collected a total of 2,734 invertebrates representing 24 taxa in 11 families. The most diverse invertebrate family was Xanthidae (six species) followed by Palaemonidae (five species). We used ordination techniques to examine variation in species relative abundance among habitats, seasons, and sampling areas, and to identify environmental gradients correlated with species relative abundances. Our resulted indicated that oyster provided a similarly complex and important function as the adjacent VME. We documented three basic trends related to the importance of oyster and VME habitats: 1) Oyster and VME provide habitat for significantly more species relative to NVB, 2) Oyster and VME provide habitat for rare species, and 3) Several species collected across multiple habitats occurred at higher abundances in oyster or VME habitat. We also found that salinity, temperature, and depth were associated with seasonal and spatial shifts in nekton communities. Lastly, we found that the relative location of the two marsh complexes we studied within the context of the whole estuary may also explain some of the temporal and spatial differences in communities. We conclude that oyster habitat supported a temporally diverse and spatially distinct nekton community and deserves further attention in research and estuarine conservation efforts.