This study investigates the Baini River Basin using the MixSIAR model to quantify nitrate contributions from wastewater effluent (M&S), sewer leakage (SL), agriculture (AG), soil nitrogen (SN), and urban runoff (UR), with flux calculation used to verify model reliability. Results show that wastewater effluent is the dominant source (67.5%), followed by soil nitrogen (13.7%), agriculture (12.6%), sewer leakage (4.7%), and urban runoff (1.1%). Source contributions show spatiotemporal variations. In the wet season, wastewater effluent accounts for 54.0%, while agriculture and soil nitrogen contribute 18.3% and 19.5%, respectively. In the normal season, wastewater effluent rises to 61.8%, while agriculture and soil nitrogen decline. Spatially, the main channel and downstream tributaries are dominated by wastewater effluent (55.4% and 57.1%), whereas agricultural input rises at the watershed boundary (25.7%). Isotopic and dissolved oxygen data indicate limited denitrification in the basin, and wastewater effluent and untreated sewage leakage are the main sources of riverine nitrogen. Therefore, sewer network maintenance, stormwater–sewage separation, and sewage overflow control should be strengthened.