The location of a stream reach relative to other landforms in a watershed is an important attribute. We hypothesized that lakes disrupt the frequency of finer, more mobile sediments and thereby change sediment transport processes such that benthic substrates are more stable (i.e., less mobile) below lakes than above lakes. In turn, we hypothesized that this reduced mobility would lead to greater periphyton biomass below lakes. We tested these hypotheses in study reaches above and below lakes in 3 mountain watersheds. To expand this comparison, we analyzed the relationship between sediment attributes and periphyton biomass in one watershed with and one watershed without a lake. We hypothesized that no clear pattern or change in sediment size or chlorophyll a (chl a) would be observed over a 3-km-long study reach without a lake. In contrast, we expected a clear discontinuity in both sediment size and chl a in a 7-km-long study reach interrupted by a lake. Average median sediment size (D₅₀) was significantly larger (p < 0.01) in lake-outlet than lake-inlet reaches (41 mm vs 10 mm). Bed sediments in lake-outlet reaches were immobile during bankfull flows, whereas sediments at lake-inlet reaches were mobile during bankfull flows. Chlorophyll a was ≥10× greater in lake-outlet reaches than in lake-inlet reaches, although this difference was not statistically significant (p = 0.17). The longitudinal analysis clearly showed geomorphic transitions in sediment size and mobility downstream of mountain lakes, and these geomorphic transitions might be associated with changes in periphyton biomass. Geomorphic transitions can alter sediment transport and should be considered in concert with other factors that are considered more commonly in benthic ecology, such as light, nutrients, and temperature.