Conservation practitioners increasingly recognize the conservation value of tributaries for supporting mainstem, large-river specialist fishes. A tributarys discharge at its mouth is a coarse indicator of large-river specialist fishes found within the tributary, but the relative influences of regional dispersal and local habitat underpinning this species-discharge relationship is often unknown. We sampled large-river specialist fishes at sites within two nonwadeable tributaries of the Missouri and Mississippi rivers with contrasting prairie (Grand River) versus upland (Meramec River) habitats to address four research questions: (1) do mean site-level species richness (alpha diversity) and beta diversity (among-site species compositional differences) vary between tributaries? (2) does mean annual discharge correlate with local habitat and downriver distance to mainstem rivers (i.e., mainstem connectivity)? (3) are slopes of species-discharge relationships consistent between tributaries? and (4) do local habitat and downriver distance explain residual richness at sites beyond variation already explained by species-discharge relationships? We detected 30 of 42 potential large-river specialist fishes, demonstrating most mainstem species use tributaries. Mean site-level richness was higher in the Grand River (12.5 species versus 9.8 species in Meramec River), but partitioning of lower reaches (sites < 116 km from river mouth) and dispersal limitation in upper reaches (sites 116 km from river mouth) caused Meramec River beta diversity to be three times higher. Mean annual discharge correlated with habitat availability at sites and downriver distance. Although site-level alpha richness increased with discharge in both tributaries, slopes of species-discharge relationships varied between tributaries. Analyzing species-discharge residuals revealed downriver distance explained additional variation in site-level richness not accounted for by local discharge. For example, discharge alone underrepresented richness in lower-discharge, accessible sites (maximum underestimate = 8.7 species) and overrepresented richness in isolated sites (maximum overestimate = 5.8 species). Thus, predictive performance of species-discharge relationships can be improved by accounting for varying habitats among tributaries and downriver distance of sites when valuing tributaries for fishes with dispersal-dependent life cycles.