Natural river-floodplain systems are characterized by their dynamic hydrology and diverse geomorphology resulting in a wide range of habitats that support high fish diversity and production. Various factors (e.g. hydrological dynamics, water quality, and biotic processes) have been proposed to explain fish distribution in large river floodplains, but it is still widely acknowledged that the mechanisms involved may vary in diverse floodplain systems and that they are not fully understood. To determine how flooding dynamics and floodplain geomorphology influence fish species distributions across the Volga-Akhtuba floodplain, Russian Federation, we examined the distributions of eight species with respect to variables reflecting floodplain hydrology and geomorphology. On the basis of fish catches in 40 floodplain water bodies at the end of summer in 2006–2008, we found that frequency of occurrence of most fish species remained stable along the time. The distribution of fish species was strongly influenced by the size and shape of water bodies as well as flood extent. Therefore, the long-term flood variability that drives the geomorphic heterogeneity of the floodplain creates suitable habitats across ranges of fish flow guilds (rheophilic, eurytopic, and limnophilic), resulting in high diversity of the floodplain ichthyofauna. We conclude that this diverse habitat availability is a highly significant factor influencing fish distribution in the Volga-Akhtuba floodplain.