River metabolism is driven by hydrological and physicochemical regimes in rivers, but these regimes are altered by a suite of stressors including anthropogenic water demand and climate change-driven drought. These stressors compound to alter the magnitude, timing, and duration of streamflow events in rivers. Despite the importance of flow regimes in regulating ecosystem processes, the effects of flow regime alteration on basal processes, such as metabolism, are poorly understood. To better understand the linkages between river alteration, metabolism, and lower trophic levels, we deployed oxygen and temperature sondes and measured benthic algae and macroinvertebrates in seven tributaries of the upper Colorado River basin with varying degrees of flow alteration during baseflow conditions in 2023 and 2024. We then used linear mixed effects models and model selection to assess environmental predictors of river metabolism, benthic algae and macroinvertebrate standing stock. Most study sites were net heterotrophic during both years of the study, except one large river that was net autotrophic in both years. Though most rivers were heterotrophic, 50% of study sites experienced periodic autotrophy (>7 days) during periods of low, steady flow. Gross primary production (GPP) and ecosystem respiration were reduced immediately following high-flow events at all study sites. Variation in GPP was best explained by light (β=0.34, SE=0.06) and an index of flow alteration (β= -0.62, SE=0.18). Variation in chlorophyll-a was best explained by an index of flow alteration (β= -0.57, SE=0.18), and variation in macroinvertebrate density was best explained by an index of flow variability (β=1.54, SE=0.70) and turbidity (β= -0.68, SE=0.26). To date, much metabolic research has neglected unique, desert river ecosystems. Improving our understanding of linkages between river alteration, environmental variables, and metabolic regimes will enhance our ability to predict how desert riverine ecosystem structure and function might change in the future.