For the past decade, oysters have been recognized as “ecosystem engineers” that generate important ecological services, including habitat provision for nektonic organisms (e.g., adult finfish, certain crustaceans). Most previous studies investigating this role of intertidal oyster reefs in South Carolina have compared the nektonic assemblages on natural oyster reefs, saltmarshes, mud bottom and subtidal oyster shell habitats using various methods which involve some degree of habitat disturbance. The present study employed a novel, non-destructive sampling method involving the deployment of a drop net around study plots to compare the nektonic assemblages associated with intertidal oyster reefs (natural and enhanced) with those of neighboring soft sediment habitats at three sites in South Carolina. Each site comprised an experimental plot, which contained an oyster reef varying in substrate type (oyster “castles”, oyster shell bags, and natural oyster reef) and age (1 to 7 years), and an adjacent control plot without structural complexity. Abundances of nektonic organisms were higher in experimental plots compared to control plots and were correlated to surface seawater temperature at all locations in the experimental plot. Species richness was significantly higher within the experimental plot than within the control plot at two of the three study sites. At the remaining site, the number of species did not differ significantly between treatments. Differences in diversity between treatments across sites may be explained by habitat age.