Physical disturbances in streams have important effects on 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 in turn benthic organisms. We assessed patterns of disturbance and recovery for metabolic processes of GPP and ER associated with periods of increased flow and suspended sediment flux between December and April in two streams in the Oregon Coast Range with differing lithologies (basalt and sandstone). The results of whole-stream metabolism modelling indicate that the two study streams have varying patterns of response and recovery rates after storm events. Both streams were heterotrophic during the entirety of the study period with changes in heterotrophy driven by changes in ER. Poststorm GPP decreased in both streams, but the basalt basin had greater proportional decreases and recovered slower than the sandstone basin. This result was unexpected and appeared to be associated with lower light availability in the basalt basin driven by increased turbidity during storm events; the coarser basalt substrate weathers into smaller size fractions than the finer sandstone substrate, remaining in suspension over longer periods and limiting light availability to benthic primary producers. The rates of ER in the sandstone basin did not change from prestorm to poststorm, whereas rates of ER in the basalt basin had varying responses. Overall, our results indicated that the underlying lithology of small mountain streams can drive variability in GPP by controlling sediment size and light availability during storms events.