We estimated past and future hydrographs and patterns of ecosystem metabolism in a fifth-order river of the western United States, where water use and climate change are both expected to alter hydrology in the immediate future. We first reconstructed the unregulated hydrograph to estimate how the current hydrograph has been altered. Due to consumptive use, 95% as irrigation, current discharge during summer (July–September) was 70% lower than would occur if the river was unregulated. We then predicted a future hydrograph including effects of consumptive use and climate change; the magnitude of flow changes were minor under this regime relative to those already manifested by consumptive uses. We used time-series regression and a six-year continuous record of open-water metabolism to demonstrate that, under the current hydrologic regime, gross primary production (GPP) was dependent on both water temperature and flow and that ecosystem respiration (ER) was most dependent on temperature. Monte Carlo simulations under the three hydrologic regimes and three temperature scenarios (current, +2°C, +4°C) suggested that flow, but not temperature, may have profound effects on the magnitude of metabolism. Linking temporally detailed analyses of ecological function and hydrology may lead to better understanding and management of changes due to basin-scale water use and/or global-scale climate change.