Anthropogenic modifications have altered aquatic communities, food web structures, and energetic pathways along rivers and within river networks. While algae and aquatic plants support lotic food webs with in-situ primary production, current understanding of spatial variability in ecosystem metabolism along a river or river network remains limited. We used dissolved oxygen measurements to estimate gross primary production (GPP) and ecosystem respiration (ER) in the oligotrophic Kootenai River and tributaries. Mainstem sites spanned 158 river km across Montana and Idaho with reaches characterized by different nutrient concentrations and channel morphology including a narrow canyon reach with limited floodplain, a braided reach with wider and shallower channel, a deeper slow moving meander reach, and a reach downstream of phosphorus addition. Tributary sites were situated along 70 mainstem river km and were characterized by different land use and channel depth. Higher GPP and ER were associated with reaches characterized by greater agricultural land use, phosphorus addition, and shallow river depths. Our results suggest that adjacent land use, river management, river morphology, and nutrient concentrations affect the timing and magnitude of GPP and ER. Understanding how ecosystem metabolism varies within a river network may provide a baseline for evaluating the effectiveness of future river management decisions intended to improve food resources for fish.