Hydrological and nitrate pollution processes are important parts of aquatic ecosystems. For this study we collected samples of river water, reservoir water, shallow groundwater, deep groundwater, and precipitation in the Fenhe River Basin. δD and δ¹⁸O were used to identify the hydrological process. δ¹⁵N-NO₃^- and δ¹⁸O-NO₃^- were used to identify the sources and pollution process of NO₃^-. The results show that precipitation is the main source of water in the study area, and there is an obvious isotopic fractionation caused by evaporation. The reservoir water, river water, soil water, and shallow groundwater had a mutual recharge and discharge association. Deep groundwater is recharged by archaic groundwater and less affected by evaporation and human activity. NO₃^- is the main N species in the study area, nitrification is the main source of NO₃^-, and denitrification is also found in some river branches. 46.2% of NO₃^--N concentrations exceeded the drinking water standard of China. NO₃^- Sources are mainly controlled by land use type. Nitrogen in precipitation and soil organic N are the major sources of NO₃^- in the upstream. The midstream area is mainly polluted by manure and sewage, while the downstream area is polluted by a mixture of soil organic N and fertilizers.