Water levels fluctuate widely in Carolina bay wetlands and most dry periodically. Aquatic organisms inhabiting these wetlands have the capacity to either resist desiccation or to recolonize newly flooded habitats. The objective of this study was to determine which invertebrates aestivate in the soil of dry Carolina bays and to describe how differences in habitat affect the composition of aestivating invertebrates. Eight Carolina bays located on the Savannah River Site (SRS) near Aiken, South Carolina, USA were examined for this study. Although all of the wetlands dried seasonally, three of the wetlands were relatively wet (inundated 47–92% of the year on average), one was intermediate, and four were relatively dry (inundated 20% of year on average). Sections of soil were removed from each bay during August and November when all sites were dry, placed into tubs, flooded, and covered with fine mesh. Invertebrates were sampled from the water biweekly for four weeks. Invertebrate assemblages were contrasted between naturally inundated bays and rehydrated samples, wetter and drier bays, August and November collections, and remnant ditches and the main basins. Common aestivating fauna included midges, dytiscid beetles, copepods, and cladocerans. The Jaccard's coefficient of similarity for invertebrates emerging from dry substrate and from naturally flooded wetlands (with both aestivators and colonizers) averaged 0.22. More taxa emerged from rehydrated samples from wetter bays than drier bays. Season affected which taxa emerged. Remnant ditches supported fewer taxa than basins. Aestivating invertebrates make up a significant component of Carolina bay fauna.