The importance of floodplain habitats to biotic communities has long been acknowledged. Many large river systems, however, are heavily regulated by dams that alter natural flood pulses and restrict large volumes of water from entering floodplains. We were interested in determining how alterations in flow regime may affect communities of fishes and invertebrates in floodplains along the Savannah River. To do so, we monitored floodplain fish and invertebrate community responses across three flow regimes: 1.) unregulated pulses (in the adjacent and free-flowing Altamaha River); 2.) controlled, released pulses in the Savannah from 2005-2006, and; 3.) the lack of released flood pulses in the Savannah from 2007-2009. We hypothesized that fish and invertebrate communities of the non-pulsed Savannah floodplains would be distinct from communities within the Altamaha floodplains, and that the pulsed Savannah floodplains would host intermediate communities. To test this hypothesis, we sampled for fishes (via backpack electro-shocker) and invertebrates (with a Hess sampler) in floodplain sites along the Savannah and Altamaha rivers during spring months from 2005 to 2009. Multivariate analysis showed modest differences in macroinvertebrate communities between floodplains of both rivers (P = 0.046) and highly distinct macroinvertebrate communities between pulsed and non-pulsed years in the Savannah (P = 0.006). Similar analysis of floodplain fish communities showed weak distinction between the Altamaha and two flow regimes of the Savannah (P = 0.050). However, larger spatial and temporal variation in fish communities of the Altamaha, and to a lesser extent in pulsed years of the Savannah, was observed. Indicator species analysis indentified pickerels (Esox sp.) and predacious diving beetles (Dytiscidae) as taxa significantly influencing community variation in the Altamaha floodplains. Reduced numbers of both taxa under low flow conditions suggest that they may serve as barometers of community health in floodplain habitats of the Savannah with regards to differing flow regimes. Highly variable communities may be the norm in floodplains, and therefore restoring flows that mimic natural flood pulses to the Savannah might result in more dynamic floodplain communities.