Water diversions are prevalent on arid land rivers worldwide, yet their impacts on riverine ecosystem processes are not well understood. We used a two decade-long data set of high-frequency dissolved O2 and water temperature from the Lower Truckee River, Nevada, USA to examine patterns of ecosystem metabolism and concomitant effects on water quality above and below a large water diversion point. Data were consistently collected during summer and fall when water quality impairment associated with low flow conditions was common. While the Derby Dam diverted between 1 and 72% of annual late summer flows (August–October mean = 39% from 2000–2023), nutrient levels remained relatively similar at the two sites, allowing us to examine how water quantity influenced river metabolism. GPP was higher at the site above than the site below the diversion (August–October mean = 9.2 and 5.0 g O2 m-2d-1, respectively). Both sites were strongly autotrophic, with > 80% of late summer days having NEP > 0, similar to other rivers with open canopies and stable summer baseflows. While the site above the diversion had decreasing summer GPP throughout the multidecadal study period, GPP did not display strong temporal trends at the site below the diversion. Summer-fall GPP did not co-vary strongly with flow at either site, despite a wide range of annual summer baseflow magnitude across the study period. Contrary to relationships between GPP and flow, NEP increased with increasing flows at both sites, which along with higher gas exchange rates at higher flows, caused dissolved O2 to remain higher than during low flows. These results show that water allocation alters water quality through biological (GPP and ER) and physical (gas exchange) processes. Understanding the effects of flow management on stream metabolism is needed to promote ecosystem processes that support water quality under continued water extraction in rivers worldwide.