Floodplain connectivity has been identified as an important element of river ecosystem function for enhancing biological productivity, yet most of the world's large rivers have been managed to reduce river–floodplain connectivity to protect human interests. Flow events in the Missouri River basin during the summers of 2010 and 2011 offered a unique opportunity to investigate the influence of floodplain connectivity on fish communities. The floods created aquatic habitats not generally available on the main stem and the magnitude and duration of the 2011 event have not occurred since the main-stem dams were closed. Therefore, the objectives were to: (1) document species use on available floodplain habitats and assess age-0 fish presence, (2) compare spatial and temporal distribution of fish species, and (3) evaluate fish community responses at different discharges. Age-0 fish dominated the fish community during the 2010 and 2011 floods, representing 90% and 94% of all fish collected each year. Species composition during the 2011 flood was different above and below the Platte and Missouri rivers confluence (ANOSIM; r = 0.211; p < 0.001) and between individual sites (r = 0.667; p < 0.001) but did not change temporally (r = 0.086; p = 0.244). Comparison of the age-0 fish community response to varying water levels also differed (r = 0.619; p = 0.038) annually. The effects of this flood on the fish community of the Missouri River initially appear to have been beneficial for the native fish community; however, continued research and evaluation will verify the flood's effects.