Biologically available nitrogen from human inputs can alter nutrient dynamics across landscapes and aquatic ecosystems. Relatively small changes in land use and river management may contribute to altered nutrient dynamics and influence denitrification and assimilatory uptake in river systems. Recent and ongoing expansion of surficial mining operations in the Elk River watershed in British Columbia (BC), Canada, has resulted in increased nitrate loading 10-fold or more in the downstream Kootenay River in BC, Koocanusa Reservoir in BC and Montana, U.S., and the mainstem Kootenai River downstream of Libby Dam in Montana and Idaho. The combination of excessive nitrate loading along with decreased phosphorus availability has skewed the N:P ratio to greater than 200:1 in both the river and reservoir. We estimated nitrate uptake over 16 years in 5 reaches of the river spanning 224 river km in Montana and Idaho, within which morphology and river enhancement efforts differ. River reaches include a tailwater section below Libby Dam, reaches upstream and downstream of a P addition site at the ID/MT border, a braided reach with habitat modifications, and a deep, slow-moving meander reach. Phosphorus addition increases nitrate uptake rates and extends the period of higher nitrate uptake rates. During 2022, we estimated continuous nitrate uptake and ecosystem metabolism to bracket the P addition reach before and during P additions. Diel fluctuations in nitrate uptake were apparent throughout the study with clear shifts from night to mid-day peaks as the biofilm established. GPP was higher in the P addition reach than an adjacent reach. Loss of transformation and removal of N indicate that the entire N load may be transported downstream at times. Nitrate saturation due to the excessive N loading would be detrimental to downstream ecosystems.