The Upper Clark Fork River (UCFR) in western Montana is part of the largest Superfund project in the United States and has undergone extensive restoration following decades of mining-related contamination. Monitoring associated with ongoing floodplain restoration activities, including contaminated sediment removal and floodplain reconnection, provides a unique opportunity to examine long-term nitrate dynamics in a heavily managed river system. This study examines how the coupling of seasonal ecosystem uptake with a snowmelt-driven hydrologic regime influences temporal and longitudinal patterns of nitrate concentrations in the UCFR. We analyzed nitrate as NO₃–N from 13 sites spanning ~200 km of the UCFR, sampled biweekly to monthly in a growing dataset from 2017 to 2024. We hypothesized that the primary controls on seasonal nitrate patterns are flushing or dilution during the snowmelt season and uptake of nutrients by algae during the growing season, and that spatial differences in nitrate loading from groundwater produce distinct concentration-discharge (C–Q) relationships along the river. We present consistent evidence from the hystereses of C–Q curves at most monitoring sites that nitrate concentrations rapidly decrease, likely due to dilution at peak flows; remain low during decreasing and warm low-flow conditions during the algal growing season with increased biological demand; and increase during cooling low flows due to higher concentrations in groundwater inputs and decreasing ecosystem uptake. The spread of these hystereses appears to increase in upstream segments of the river, where groundwater nitrate loading is stronger, and then decrease downstream where groundwater nitrate loading is weaker. Comparisons of two UCFR tributaries representing contrasting land-use influences provide some evidence that sites with very low nitrate loading from groundwater may exhibit little to no hysteresis and either chemostasis or a modest flushing effect of higher nitrate concentrations at high flows. Together, these results demonstrate how hydrology, nitrate loading, and biological uptake interact to control nitrate dynamics in a recovering river system with a snowmelt-dominated hydrologic regime.