Aquatic habitats are among the worlds most valuable ecosystems, including rivers and floodplains. Humans have significantly influenced these ecosystems the world over, particularly in the form of river regulation via dams. The objective of this dissertation is to document effects of river regulation in rivers and floodplains of the southeastern United States. Specifically, I focused on the effects of river regulation on macroinvertebrate dynamics in the Chattahoochee, Altamaha, and Savannah Rivers (Georgia). Direct effects of annual and daily flow variation on the macroinvertebrate communities of the Chattahoochee River below Buford Dam were investigated over an 11 year period. In addition, to assess indirect effects of river regulation, I investigated populations of predaceous diving beetles (Coleoptera: Dytiscidae: Neoporus) on the floodplains of the regulated Savannah River and the unregulated Altamaha River. The results from my research indicate significant effects of regulation within the river channel and across the floodplains. Shifts in macroinvertebrate community assemblages were detected between high- and low-flow years on the Chattahoochee, and changes to the overall community occurred over the length of the study area, with improved biological metric scores (H, EPT richness, and sensitive taxa richness) as distance from the dam increased. On floodplains, Neoporus beetles exhibited significant sympatry but were overall negatively affected regarding their distribution and propensity for flight as a result of river regulation. With little overbank flooding in the regulated system, Neoporus were more likely to be restricted to permanent waters on the floodplain and were less likely to disperse via flight than populations in the unregulated system. These results suggest a need for altered river management strategies where ecosystem integrity is taken into account in addition to human needs. River management strategies should be developed in the context of climate change and increasing pressures on water resources.