Understanding linkages among fluvial geomorphology, habitat, and aquatic biota is critical for effective stream ecosystem conservation. However, composite effects of hydrogeomorphic adjustment and condition, which collectively represent channel stability, on freshwater mussel and stream fish assemblages remain unresolved. Associations between stream hydrogeomorphic characteristics (channel geometry, substrate composition, stream flow) and mussel and stream fish assemblages were explored at 20 study reaches characterized by riffle–pool interfaces (RPIs) in Ohio, USA. At a coarse resolution using categorical classifications of equilibrium (i.e. stable) vs. adjusting (i.e. unstable) RPIs, overall fish and darter density was greater at adjusting RPIs (P = 0.048 and P = 0.024, respectively). Conversely, fish species richness was 1.2× greater at equilibrium than adjusting RPIs (P = 0.047). Analysis of quantitative hydrogeomorphic data collected with fine‐resolution surveys showed that hydrogeomorphic parameters explained from 20% (darter assemblage evenness) to 55% (density of mussels known to use darters as hosts) of the variation observed in all assemblages. Drainage area was significant in most models with variable influence: R2 = 0.10 for darter species richness to R2 = 0.41 for Simpson's diversity index of mussels with darter hosts. Other important predictor variables included embeddedness, velocity, shear stress, roughness, channel dimensions, and sediment size. Whereas coarse‐level fluvial geomorphic classifications may be meaningful for fish, they appear less so for mussels. Fine‐resolution quantitative hydrogeomorphic variables provided substantially more information for both assemblages, although hydrogeomorphology–fish and hydrogeomorphology–mussel relationships were not consistent. Some of the strongest relationships related to mussels that use darters as hosts, suggesting that these species are particularly sensitive to hydrogeomorphic conditions. Collectively, these results indicate that fluvial geomorphic condition and characteristics can simultaneously influence co‐dependent stream biota. Stream conservation and management plans that include explicit hydrogeomorphic surveys may appreciably benefit cohabitating freshwater fish and mussel assemblages. Copyright © 2014 John Wiley & Sons, Ltd.