Aerobic respiration of organic matter is a key metabolic process influencing carbon (C) biogeochemistry in aquatic ecosystems. Anthropogenic and environmental perturbations to stream ecosystem metabolism can have deleterious effects on downstream water quality. Various environmental features of rivers also influence stream metabolism, including physical (e.g., discharge, light, flow regimes) and chemical factors (nutrients, organic matter) and watershed characteristics (e.g., stream size or drainage area, land use). The relative proportion of surface water contact with benthic sediments has been considered the primary driver of ecosystem processes, including ecosystem respiration (ER). While aquatic ecosystem respiration occurs in the water column (ER_wc) and in benthic sediments—including surficial and subsurface sediments (ER_sed)—ER_sed has long been assumed to be the primary contributor to whole-river ecosystem respiration (ER_tot). Recent studies show, however, that somewhere along the river continuum (e.g., 5^th–9^th order), rivers transition from being dominated by benthic processes to being dominated by water column processes. Yet few metabolism studies have parsed contributions from the water column (ER_wc) to ER_tot, making it difficult to evaluate the relative magnitude and importance of ER_wc across the river continuum and across biomes. In this study, we used the Yakima River basin, Washington, USA, to increase our understanding of basin-scale variation in ER_wc. We collected ER_wc data and water chemistry samples in triplicate at 47 sites in the Yakima River basin distributed across Strahler stream orders 2–7 and different hydrological and biophysical settings during summer baseflow conditions in 2021. We found that observed ER_wc rates were consistently slow throughout the basin during baseflow conditions, ranging from −0.11–0.03 mg O₂ L⁻¹ d⁻¹, and were generally at the very slow end of the range of published ER_wc literature values. When compared to reach-scale ER_tot rates predicted for rivers across the conterminous United States (CONUS), the very slow ER_wc rates we observed throughout the Yakima River basin indicate that ER_wc is likely a small component of ER_tot in this basin. Despite these slow rates, ER_wc nonetheless shows spatial variation across the Yakima River basin that was well explained by watershed characteristics and water chemistry. Multiple linear regression model results show that nitrate (NO₃-N), dissolved organic carbon (DOC), and temperature together explained 41.5 % of the spatial variation in ER_wc. Supporting the findings of other studies, we found that ER_wc increased linearly with increasing NO₃-N, increasing DOC, and increasing temperature. We hypothesize that low concentrations of nutrients, DOC, and low temperatures in the water column, coupled with low TSS concentrations, likely contribute to the slow ER_wc rates observed throughout the Yakima River basin. Because ER_tot measurements integrate contributions from water column respiration and sediment-associated respiration (ER_sed), estimating ER_tot in cold, clear, low nutrient rivers like those in the Yakima River basin with very slow ER_wc will essentially measure contributions from ER_sed.