The purpose of this work is to study the effect of a type of water-saving irrigation (WSI) on nutrient runoff of paddy field. The volume of surface drainage was maintained low by WSI. In particular, WSI effectively reduced surface drainage in rain events. Model simulation indicated that net runoff load of total nitrogen (TN) from the paddy field was increased by WSI. Meanwhile, net runoff loads of total phosphorus (TP) and total organic carbon (TOC) from the paddy field was decreased by WSI. Because ponding waters of the study fields were enriched with TP and TOC, WSI reduced runoff of these nutrients by controlling the volume of surface drainage. WSI could be considered an efficient method for reducing runoff loads and could conserve water quality in an agricultural watershed.