The effect of fertilizer application on ponded and percolation water in paddies were evaluated at the field plots of the Chungbuk National University for irrigation period. The chemical fertilizers were applied to the study plots at an average application rate of 77, 110, 165kgN/ha, respectively. The concentration of T-N, T-P and COD in ponded water was high after fertilizing but greatly decreased with time. The concentration of ponded water greatly depends on the amount and timing of fertilizer applied. Therefore, the decrease in the amount of fertilizer and proper water management may be needed to reduce the runoff loading.