Physical disturbance in streams has important effects on the metabolic rates of gross primary production (GPP) and ecosystem respiration (ER). Underlying lithology can control sediment size, amount, and evolution in the stream, influencing substrate stability and its effect on benthic organisms. We assessed the patterns of disturbance and recovery of metabolic rates after periods of increased flow and suspended sediment flux in different lithologies. We modeled whole-stream metabolism during the winter-spring period between December and April in two streams in the Oregon Coast Range: one with basalt lithology, and one with sandstone lithology. Our results indicated that the two streams varied in their patterns of response and recovery to storms. Both streams were heterotrophic during the entirety of the study period, but changes in heterotrophy were driven by changes in ER. Post-storm GPP decreased in both streams, but the basalt basin had greater proportional decreases. Decreases were also greater later in the study period, when pre-storm rates of GPP were higher. Rates of ER increased in the basalt basin post-storm and did not change from pre- to post-storm in the sandstone basin. Recovery of GPP was more rapid in the sandstone basin than the basalt basin. The P/R ratio recovery period was similar in both streams, but recovery was faster in the sandstone basin. Overall, our results indicated that the underlying lithology of small mountain streams drives variability in heterotrophy through differing effects on ER.