It is widely acknowledged that efforts aimed at conserving water quality have resulted in a decrease in the inflow load to Lake Biwa. However, significant concerns have been raised regarding the reliability of the “unit-load” approach upon which this assumption is predicated. To address this issue, our study enhances the existing hydrological and substance cycle model for the Lake Biwa basin by incorporating additional functionalities. These enhancements enable us to assess the historical change of the inflow load and compare it with the traditional unit-load method. The model incorporates Total Organic Carbon (TOC) for organic matter, integrates a model for Suspended Solids (SS) generation, and includes mechanisms for change in forms and substance decomposition processes. Our findings suggest that the rate of load reduction over time was significantly slower compared to the unit-load method. This is because the model effectively calculates variations in meteorological conditions, purification and sedimentation processes, as well as load from nonpoint sources during rainfall events. The results indicate that future climate change may lead to an increase in inflow load.