We examined how substrate and complex hydraulic variables limit the distribution of freshwater mussels. We sampled mussels and measured substrate and hydraulic variables (at low and high flows) at 6 sites in the Little River, Oklahoma. To test which variables were most limiting to mussel species richness and abundance, we evaluated univariate and multiple 95^th-, 90^th-, and 85^th-quantile regression models using a model selection approach. Across all 3 quantiles analyzed, hydraulic variables related to substrate stability (relative shear stress ratio [RSS] and shear stress) at high flows most limited mussel species richness and abundance. High-flow substrate stability models performed the best, but models that used substrate variables (substrate size and heterogeneity) also performed relatively well. Models that used complex hydraulic variables estimated at low flows performed poorly compared to those using the same variables estimated at high flows, a result suggesting that hydraulic conditions at low flows do not limit mussel habitat in our system. Our results demonstrate that substrate stability at high flows is an important factor governing mussel distributions. Last, our quantile regression approach successfully quantified the limiting-factor relationships of substrate and hydraulic characteristics on mussel habitat, and this approach could be used in other studies investigating habitat requirements of aquatic organisms.