Both fine- and coarse-scale physicochemical conditions affect the quantity and quality of nursery habitats within riverine ecosystems. Nursery habitats in large, braided, and sandbed streams such as the lower Red River of Oklahoma, Texas, and Arkansas are not well described and likely vary among species. Identification of nursery habitats is important for developing proper conservation and management actions. We used an occupancy model framework to determine how hierarchical habitat factors related to the occupancy of 38 juvenile fish species. Our findings indicate that large river nursery habitats can generally be defined by reaches with off-channel slackwater habitat, having deep pools but shallow thalweg depths, typically located further away from dams, and with low percentages of limestone lithology. Species within the same genera often exhibited variable relationships with river slope, amount of large woody debris, channel shape, discharge, and position of reaches within the stream network. Our results indicate important species-specific relationships that define nursery habitats, indicating an important context dependency of nursery habitats even within fishes that are taxonomically similar. If the goal is to improve recruitment by native fishes, then consideration of the important species-specific differences would be beneficial if improvements are made to nursery habitats. Moreover, careful consideration of the effects of dam operations will help maintain proper connectivity to off-channel habitats important in downriver portions of the river network.