The Yodo River, which has two big tributaries and an annual mean flow of 268m³/s, flows out of Lake Biwa, runs through the Amagase Dam and flows into Osaka Bay. Point and non-point pollutant loads in Kyoto City and its adjacent cities discharge into the river. The frequency of our routine observation (once every three days) during the period from late April to late November 2003-2005 was ten times that of official routine water quality monitoring in Japan. We also carried flooding-stage observations at three transverse points across the river during the routine observation period in 2005. The total pollutant loads during five flooding events were larger than those observed by the routine observation during the periods. The mean pollutant loads during observation periods of every three days, every six days, every nine days and semimonthly data were different from those derived from monthly data. The annual total loads of runoff pollutant in 2003-2005 were estimated by extrapolating to both sides of the observation period and by compensating during flooding-stages using regression equations between flow and pollutant loadings.