A previous study has demonstrated that Danshui River has almost the highest dissolved inorganic nitrogen (DIN) yield in the world and exports most of the DIN in the form of ammonium unlike the world's large rivers. However, the DIN sources are poorly constrained. In this study, the contributions of major sources in the Taipei metropolitan area to the DIN export in the Danshui River were investigated. It is observed that ammonium is the major DIN species in the downstream reaches, resulting from the ammonium-dominated inputs of the effluents of wastewater treatment plants (WWTP) and rain water pumping stations (RWPS). DIN concentrations in the downstream (urban) reaches are substantially elevated. The upstream tributaries annually discharge similar to 2709 t DIN to the downstream reaches. However, the DIN discharge off the downstream reaches rises to similar to 17,918 t, resulting from the contribution of RWPS-collected water, i.e., similar to 14,632 t, and the effluents of two WWTP, i.e., similar to 577 t. RWPS-collected water inherently contains the contribution of atmospheric deposition, similar to 2937 t DIN. This finding implies that similar to 11,695 t (similar to 66 % of the downstream output) DIN flux off the Danshui River is from urban runoff and can be attributed to human activities in the Taipei metropolitan area. To improve the water quality in the Danshui River, water quality controls in urban runoff are important.