Great Plains rivers are characterized by unpredictable, thunderstorm-generated flow events that can abruptly restructure their physical complexity. These morphodynamic disturbances force river organisms to overcome hydrologic challenges. Some organisms surmount these challenges by using refugia, which play a key role in the ecological processes that govern lotic systems. The physical complexity of rivers can determine the availability and diversity of refugia both within and among rivers. However, physical complexity often changes with the hydrologic cycle and position along the river. We determined how the benthic community was affected by changes in the structure and abundance of in-channel refugia created by hydrologic fluctuations. We worked on and around sandbars in the Kansas River (Kaw), a multithread, sand-bed river. The composition of the zoobenthic community was directly related to the complexity of river morphology and flow rates. The community of 1 side channel consistently shifted over time between 2 distinct assemblages depending on whether the side channel was flowing or a disconnected slackwater. The benthic invertebrate community exploits many strategies to survive in the abrasive and continually fluctuating Kaw, including using sandbars as refugia and places for recolonization. The refuge provided by these sandbars will become increasingly important in the future if precipitation regimes become more variable as predicted by climate-change scenarios for the region. However, increased levee and dam construction threaten the persistence of the sandbars and vital habitats that they create.