Understanding how lotic communities respond to combinations and gradients of physical disturbance and nutrient inputs is important for the practical management of stream ecosystems, and to add to our knowledge of stream ecology. We used covariance structure analysis to examine the direct and indirect effects of a gradient in nutrient concentration and hydrologic disturbance on benthic community structure in 133 riffles in 97 midwestern US streams. Model results indicated that the relationship between nutrient concentration, algal biomass, and primary consumer biomass was mediated by hydrologic regime. Algal biomass was strongly dependent on nutrient supply in streams where scouring floods reduced primary consumer biomass. In more stable streams, primary consumers depressed algal standing stocks regardless of nutrient concentration. Our results imply that the response of stream benthic communities to nutrient stimulation is highly variable and dependent on physiography and climate because they strongly influence hydrologic disturbance regimes.