Composted livestock manure (referred to as compost) with a high nutrient concentration is a widely used organic input in organic farming systems. Due to the lack of guideline for standard application rate of compost, however, it tends to be applied at a rate over the crop nutrient requirement. In this context, paddy applied with compost may affect surface water quality more adversely than paddy receiving synthetic fertilizer at the standard rate. As drainage water quality is directly affected by that of floodwater in paddy, comparison of pollutant concentration in floodwater between synthetic fertilizer (conventional) and compost (organic) application could provide some insight into whether organic farming using compost is truly environment-friendly in terms of water pollution or not. Overall, Total N concentration was significantly higher in the fertilizer than in the compost treatments up to 2 weeks of basal fertilization, thereafter such difference was not observed. Meanwhile, TP and COD concentration were higher in the compost than in the fertilizer treatments up to 4 weeks of basal fertilization. Our study shows that compost application can decrease N loss but increase P loss via surface run-off and further suggests that a fertilization strategy to reduce P efflux that is the limiting factor of eutrophication from compost-applied paddy should be developed.