River nitrate (NO3–) pollution is a global environmental issue. Recently, high NO3– levels in some pristine or minimally-disturbed rivers were reported, but their drivers remain unclear. This study integrated river isotopes (δ18O/δ15N-NO3– and δD/18O-H2O), 15N pairing experiments, and qPCR to reveal the processes driving the high NO3– levels in a nearly pristine forest river on the Qinghai-Tibet Plateau. The river isotopes suggested that, at the catchment scale, NO3– removal was prevalent in summer, but weak in winter. The pristine forest soils contributed more than 90 % of the riverine NO3–, indicating the high NO3– backgrounds. The release of soil NO3– to the river was “transport-limited” in both seasons, i.e., the NO3– production/stock in the soils exceeded the capacity of hydrological NO3– leaching. In summer, this regime and the NO3–-plentiful conditions in the soils associated with the strong NO3– nitrification led to the high riverine NO3– levels. While the in-soil nitrification was weak in winter, the leaching of legacy NO3– resulted in the consistently high NO3– levels. This study provides insights into the reasons for high NO3– levels in pristine or minimally-disturbed rivers worldwide and highlights the necessity to consider NO3– backgrounds when evaluating anthropogenic NO3– pollution in rivers.