The effect of fertiltzer application on ponded and percolation water in rice paddy were investigated at the experimental plots during irrigation period. We laid out three experimental plots such as 150% Excessive, 100% Standard and 70% Reduced. The concentration of T-N and T-P in ponded water were increased rapidly after application. The concentration of T-N and COD in percolated water increased with fertilizer application rates, while T-P concentration were almost constant.