Agricultural non-point source pollution is the main cause of water quality deterioration in Erhai Lake, where 97% of total nitrogen (N) input is from non-point source. This study investigated the effect of applying different types of fertilizers (no fertilizer, conventional chemical fertilizer, combinations of organic and inorganic fertilizers, and a slow-release fertilizer) in paddy fields on N losses in surface runoff water. Applying the slow-release fertilizer resulted in the highest (p < 0.05) rice grain yield while the treatment receiving no fertilizer had the least grain yield. When compared to the conventional fertilizer treatment (CK), application of slow-release fertilizer reduced the concentrations of total nitrogen, ammonium nitrogen, and nitrate nitrogen in the surface runoff by 45, 66, and 55% (p < 0.05), respectively. The treatment used slow release fertilizer also reduced the surface runoff losses of total nitrogen, ammonium nitrogen, and nitrate nitrogen by 47, 67 and 54%, respectively.