To understand the phenomena occurring in Lake Biwa and predict the effects of measures for improving water quality, constructing a simulation model that can calculate the hydrological and material cycle and reaction process in the basin with high accuracy is the most effective way. In this study, a Lake Biwa Basin simulation model with the integration of three components of land, lake flow, and lake ecosystem is constructed and named "Lake Biwa Basin Hydrological and Material Cycle Simulation Model". Distributed and 3-dimensional models are adopted; these models can simulate water quality and quantity unsteadily by considering weather, social conditions, and so on. As a result, river discharge and quality in main rivers, such as Yasu River and Hino River, and water temperature, average quality and seasonal variation in the lake are adequately calculated. On the other hand, it is insufficient to calculate water quality of the time series and distribution in Southern Lake; thus, it is a future challenge to evaluate spatial-temporal lake water quality precisely.