Both endangered and non-endangered unionid mussels are heterogeneously distributed within the Allegheny River, Pennsylvania. Mussel populations vary from high to low density downstream of Kinzua Dam, and the direction, amount, and range of hyporheic exchange (seepage) at the sediment–water interface were suspected to influence their distribution and abundance. Nineteen hydrogeomorphic variables, including the quantification of seepage metrics, substrate size, river stage, river discharge, and shear stress, were measured at five reaches on the Allegheny River within 80 km downstream of Kinzua Dam. Analysis revealed significant (α = 0·05) non-linear correlations between mussel population density and directional mean seepage (positive relationship), river width (positive relationship), and median substrate size (negative relationship). Specifically, seepage findings showed that increases in upward seepage and decreases in the overall range of seepage related to increases in mussel population density. River width, directional mean seepage, and median substrate size were also found to co-vary with marginal significance (α = 0·1), making their individual influences on mussel population density uncertain. Absolute mean seepage, water depth, hydraulic head, temperature differences between the surface water and substrate, and other substrate metrics besides median grain size were not found to significantly correlate to mussel population density. Considering the physical processes often linking seepage to other explanatory variables, future research in seepage–mussel relationships should work to isolate the mechanistic influence of hyporheic exchange independently from its common covariation with substrate size and geomorphology. Copyright © 2014 John Wiley & Sons, Ltd.