Most of the backwater habitat in the floodplain of the lower Missouri River has been eliminated, but the lower reaches of tributaries have flow and depth characteristics similar to backwaters. We sampled the assemblages of fish larvae and age‐0 juveniles in the lower 8 km of four tributaries and in the Missouri River main channel to determine the extent to which riverine species use these backwaters for early life history stages. We also sought to determine which tributary characteristics were associated with use by riverine species. Densities of 8 of the 10 fish taxa analyzed were greater in tributaries than in the Missouri River in 1987 and 1988. The composition of the larval fish fauna varied: carpsuckers Carpiodes spp., goldeye Hiodon alosoides, freshwater drum Aplodinotus grunniens, and common carp Cyprinus carpio occurred in large rivers; whereas mostly gizzard shad Dorsosoma cepedianum, nearctic cyprinids (mostly emerald shiner Notropis atherinoides and red shiner Cyprinella lutrensis), and sunfishes Lepomis spp. occurred in small tributaries. Assemblages in large tributaries included large‐river and small‐tributary taxa. The gradient in assemblage composition, from small‐tributary fauna to large‐river fauna, corresponded to a gradient in channel morphometry, from shallow waters and coarse substrate to greater channel depths and fine sediments. The complex pattern of flow between the Missouri River and its tributaries and the diversity of tributary morphometry were associated with, and may be critical to, productivity and the maintenance of a diverse fish fauna.

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