Lake Biwa is the largest lake in Japan, and water quality in the lake is heterogeneous. Therefore, it is important for water quality management that spatial distribution of water quality in the lake should be clearly understood. The objectives of this study are to show a methodology and to develop a simulation system to calculate COD distribution in Lake Biwa taking internal COD production into consideration. This study also aims to examine transition of COD in the lake using the simulation system. In the simulation system, runoff loads of COD from the Lake Biwa basin are calculated by Macro Model for each tributary. The external COD concentration in 233 inshore meshes of the Lake Biwa water surface was calculated using the runoff loads. The internal COD was calculated using relationships among limiting nutrients, chlorophyll-a and COD. Then, the spatial distribution of water quality in Lake Biwa was calculated both for the external and internal COD by spline technique. Simulations using the system were implemented for 1986-1998, and a clear difference in characteristics between a drought year and a flood year was shown. In the result, it was shown that the simulation system developed here was available to calculate COD distribution in Lake Biwa, and that it had the possibility to explain the recent phenomenon of COD increase in the lake.