Elevated riverine nitrate (NO3−) levels have led to increased eutrophication and other ecological implications. While high riverine NO3− levels were generally ascribed to anthropogenic activities, high NO3− levels in some pristine or minimally disturbed rivers were reported. The drivers of these unexpectedly high NO3− levels remain unclear. This study combined natural abundance isotopes, 15N-labeling techniques, and molecular techniques to reveal the processes driving the high NO3− levels in a sparsely populated forest river. The natural abundance isotopes revealed that the NO3− was mainly from soil sources and that NO3− removal processes were insignificant. The 15N-labeling experiments also quantitatively showed that the biological NO3− removal processes, i.e., denitrification, dissimilatory NO3− reduction to ammonium (DNRA), and anaerobic ammonia oxidation (anammox), in the soils and sediments were weak relative to nitrification in summer. While nitrification was minor in winter, the NO3− removal was insignificant relative to the large NO3− stock in the catchment. Stepwise multiple regression analyses and structural equation models revealed that in summer, nitrification in the soils was regulated by the amoA-AOB gene abundances and NH4+-N contents. Low temperature constrained nitrification in winter. Denitrification was largely controlled by moisture content in both seasons, and anammox and DNRA could be explained by the competition with nitrification and denitrification on their substrate (nitrite-NO2−). We also revealed the strong hydrological control on the transport of soil NO3− to the river. This study effectively revealed the mechanisms underlying the high NO3− levels in a nearly pristine river, which has implications for the understanding of riverine NO3− levels worldwide.