A dual-isotope and solute flux mass-balance was used to elucidate the processes that lead to attenuation of nitrogen contamination in an agriculturally impacted river. The River Wensum drains a lowland catchment with an area of 570 km2 in East Anglia, eastern England. Analysis of nitrate concentration, δ15NNO3 and δ18ONO3 of samples from the River Wensum collected from upstream locations to the catchment outlet through all seasons and flow conditions showed a consistent pattern of increasing isotope values with decreasing nitrate concentrations downstream. δ15N NO3 and d18ONO3 of catchment surface water and groundwater samples revealed a dominant influence from microbially cycled and nitrified source-nitrogen, which results in high nitrate concentrations in Chalk groundwater and upstream in the River Wensum. Denitrification of Chalk groundwater-baseflow in the hyporheic zone results in the downstream trend observed in the river. Hyporheic denitrification is estimated to remove 931 kg/day of nitrate-nitrogen by the catchment outlet, representing 31% of the potential riverine nitrate load. The use of dual-isotope and solute flux modeling at the catchment scale is a novel application to quantify denitrification within the river valley, demonstrating the importance of hyporheic zone processes in attenuating the impacts of anthropogenic contamination of hydrologic systems.