In the Kinokawa river basin, as same as other watersheds around the world, excess runoff of nutrients to the ocean mainly due to human activities has become an environmental issue. This study conducted high-frequency total nitrogen (TN) and total phosphorus (TP) monitoring at several monitoring posts set downstream of the Kinokawa river in the Kii peninsula, Japan in order to evaluate water pollutant load from the basin quantitatively. The water sampling has been conducted about 90 times for over a year from May in 2018 at the monitoring posts. In the calm or the drought periods, TN and TP concentrations at Kinokawa river mouth were basically about 0.8 similar to 1.1 mg/L and under 0.05 mg/L, respectively. However, TN concentrations was exceeded 5.0 mg/L after one of the most intense storms, it was shown the TN concentration had a tendency extremely to rise rapidly in flooding condition. This tendency was similar in TP. The result of pollutant load analysis showed that 65% of the nitrogen load and 80 % of the phosphorus load from the basin was generated during a few and heavy flooding which were included in 5 % flow exceedance probability. These results imply it is essential that to understand and to predict how nutrients runoff in short-term during flooding events in order to accurately grasp long-term nutrient runoff amount.