There are increasing concerns in nitrogen (N) pollution worldwide, especially in aquatic ecosystems, and thus quantifying its sources in waterways is critical for pollution prevention and control. In this study, we investigated the spatio-temporal variabilities of inorganic N concentration (i.e., NO3−, NH4+) and total dissolved N (TDN) and identified their sources in waters and suspended matters using an isotopical approach in the Jinshui River, a river with a length of 87 km in the monsoon-climate region of China. The spatio-temporal inorganic N concentrations differed significantly along the longitudinal gradient in the river network. The NO3?, NH4+ and TDN concentrations ranged from 0.02 to 1.12 mg l− 1, 0.03 to 4.28 mg l− 1, and 0.33 to 2.78 mg l− 1, respectively.The 15N tracing studies demonstrated that N in suspended organic matter was in the form of suspended particulate nitrogen (SPN) and was primarily from atmospheric deposition and agricultural fertilizer. In contrast, N in stream waters was mainly in the form of nitrate and was from atmospheric deposition, fertilizers, soil, and sewage. Meanwhile, both δ15N-SPN and δ15N-NO3− peaked in the rainy season (i.e., July) because of higher terrigenous sources via rain runoff, demonstrating the dominant diffusive N sources in the catchment. Thus, our results could provide critical information on N pollution control and sustainable watershed management of the riverine ecosystem in monsoon-climate region.