Lake Kojima, an artificial lake located in the coastal area of western Japan, is categorized as a hyper eutrophic lake due to the nutrient inputs from the Sasagase River, Kurashiki River and Kamo River. The input nutrient loads from the rivers have never been assessed because there are no observation stations for runoff rate. The objective of this study is to confirm the total nitrogen (T-N) and total phosphorus (T-P) loads into Lake Kojima using the SWAT model for 60 years and considering changes in land use and the amount of domestic wastewater in the watersheds. Estimation results show that more than 90% of the total nutrient load comes from the Sasagase and Kurashiki rivers. The estimated T-N and T-P loads indicated two different trends in the rivers; an increasing trend is found during the period from 1950 to 1980, while a decreasing trend is found during the period from 1980 to 2009. It was suggested that the increasing trend was commonly caused by the combined effects of increase of the amount of domestic wastewater and agricultural wastewater in the watersheds, while the decreasing trend was caused by the expansion of domestic wastewater treatment and decrease of agricultural land use. The contribution ratio of domestic wastewater to the total amount of nutrient load was estimated to be 60% in Sasagase River and 15% in Kurashiki River because the treatment ratio of domestic wastewater in Kurashiki River was higher than in Sasagase River.