A 4-year data set of continuous monitoring of suspended matter and nutrients concentration has been analyzed to evaluate the inter-annual variability and the effects of flood events on the sediment transport and nitrogen, phosphorus loadings from the Yahagi River to Chita Bay, Japan. Nitrogen was mainly loaded in dissolved form, which accounted for 59% to 88% of the annual loads, while phosphorus was mainly loaded in particulate form (45% to 78%). Loads of suspended matter and total phosphorus (T-P) by the historical flood event of the Tokai Heavy Rainfall accounted for 83% and 65% of the annual loads, respectively. Particulate phosphorus (PP) load by the Tokai Heavy Rainfall accounted for up to 1.1 to 3.2 times of the annual T-P load of the other years. Molar ratio of dissolved total nitrogen (DTN) load to dissolved total phosphorus (DTP) load during the observation period varied from 29.5 to 41.1, while the ratio of total nitrogen (T-N) load to T-P load was relatively lower (10.9 to 23.8). The concentrated load of suspended matter which occurs during flood events is found to have a great impact on the nutrients runoff to the coastal sea both in quality and quantity.