Riverine floodplain connections with the main channel are considered key influences on macroinvertebrate assemblages and their distributions. These connections increase habitat and food resource availability, but flooding also imposes stress on macroinvertebrates. We collected macroinvertebrates during the rising and falling limbs of 11 flood pulses in both river and the floodplain habitats along the length of the lower Ogeechee River (Coastal Plain reaches), including both the normal Winter-Spring flood season as well as the tropical storm season. Macroinvertebrate assemblages were mostly influenced by differences between the river and the floodplain, and assemblage turnover was high. In the river channel, assemblages were mainly influenced by the location down the watershed, and by seasonal change (with several indicator taxa unexpectedly being terrestrial invertebrates). In the floodplain, assemblages were also mainly influenced by site location, but also by pulse size. The floodplain indicator taxa for the larger pulses were terrestrial taxa while those for smaller pulses were aquatic. While most taxa, both in the river and on the floodplain, were shared among habitats and sites across the coastal plain, there were some site-specific indicator taxa. As extreme flood and drought events become more frequent in the future, it is important to better understand macroinvertebrate distributions and their resiliency to hydrologic changes in river channels and their floodplains.