Non-point source pollutant loads in Saemangeum basin are predicted to increase gradually. This study was carried out to investigate the runoff characteristics of non-point source pollution by chemical fertilizers on paddy in Saemangeum basin. The treatment was the type of chemical fertilizers; 1) customized fertilizer, 2) controlled release fertilizer, and 3) control. The treatments were replicated between 2011 and 2012. At vegetative growth period, the precipitation was greater in 2011, but rice was received less hours of bright sunshine. However, more precipitation and less hour of bright sunshine was received between heading period and grain filling period in 2012. Total inflow was 1,721 and 1,639mm and total outflow was 1,615 and 1,529mm in 2011 and 2012, respectively. Regardless of experiment year, most of inflow was caused by precipitation and outflow was caused mostly by surface runoff. Total nitrogen in paddy water was significantly higher at early stage, which may be caused by rotary tillage and fertilizer release. Total nitrogen content in water was decreased by irrigation and precipitation. Load of nitrogen runoff in 2011 was greater in customized fertilizer treatment (26.8 kg/ha) compared to controlled release fertilizer (18.4 kg/ha) and controll (13.2 kg/ha). Load of nitrogen runoff in 2012 was significantly decreased compared to 2011 due to the runoff time and precipitation. Fertilizer and plant was the main factor for nitrogen nutrient balance. Rice yield was greatest with customized fertilizer in both growing years. This study showed that the controlled release fertilizer can reduce nitrogen outflow load by 31% compared to customized fertilizer, although the 10% of yield reduction was expected under controlled release fertilizer treatment. Precipitation and runoff time was also significantly influenced on the load of nitrogen runoff.