Among freshwater systems, coldwater habitats are among the most threatened by climate change. Examining the impacts of increasing water temperature requires the use of both traditional biomonitoring efforts and measures of ecosystem function and structure. We examined fish and macroinvertebrate communities, leaf decomposition rates, periphyton production, and ecosystem metabolism to compare two branches of a trout stream in Minnesota with differing thermal regimes. The cooler South Branch had more coldwater fish, a higher index of biological integrity for fish but a lower index for macroinvertebrates. There were no differences in leaf decomposition rates between branches, although nonnative buckthorn leaves decomposed faster than native black cherry leaves. Periphyton production was higher in the North Branch than the South Branch. Both branches had high nitrogen but low phosphorus levels. Nutrient enrichment with phosphorus enhanced periphyton production in both branches. Measures of stream metabolism, based on diurnal variation in oxygen levels, showed that both branches were heterotrophic. Despite higher periphyton production in the North Branch, gross primary production was higher in the South Branch. The bioassessment measures used in our study yielded inconsistent results, pointing to the need for multiple methods to examine and better describe potential responses to warming from climate change.