One of the largest river restoration and remediation projects in the U.S. has been underway for over a decade in the Upper Clark Fork River (UCFR), Montana. The primary goal of the project is twofold: to remove heavy metal-contaminated sediments from the UCFR floodplain and to restore connectivity between the river channel and its floodplain. To track the progress of the UCFR’s recovery, we have monitored water quality and algal biomass at 13 sites along the river corridor between 2017 and 2022. These sites vary in channel size, algal community composition, and restoration status (completed, ongoing, or pending restoration). Here, we focus on how floodplain restoration is altering the river's capacity to process nutrients (nitrogen and phosphorus) by enhancing river-floodplain connectivity. Using both 20 years of historical data and contemporary monitoring, we characterize nutrient processing domains (NPDs) along the restored and unrestored reaches in the UCFR. NPDs integrate nutrient delivery (routing) and local nutrient transformation (benthic uptake) processes over time and space. We find that hydraulic loads in the upstream sections of the UCFR, where restoration efforts are more advanced, are 2-4 times higher after snowmelt-driven floods. At the same time, restoration activities are beginning to show effects downstream, with a shift in net nutrient exchange rates from positive (7.6 mg N/m²/d pre-restoration) to negative (-12.1 mg N/m²/d during and post-restoration). These shifts represent a transition from net nitrogen accumulation to net nitrogen loss in the river. Multiple reaches of the UCFR exhibit contrasting nutrient processing domains for soluble reactive nitrogen and phosphorus, shifting between nutrient sinks and sources over time. The spatial patterns of restoration progress, combined with the dynamic nature of NPDs in these reaches, offer a unique opportunity to explore the controls and consequences of biogeochemical mosaics in river ecosystems.