Lake Ogawara, located in Northern Japan, is a brackish lake with the surface-area of 63km^2. The maximum depth is about 25m, and approximately 12psu of salt water exists in a lower layer under the depth of 20m throughout the year. Lots of Corbicula Japonica are living in the lake, and about 2500 tons are taken out as fishery product. We develop an ecological model to consider the biochemical processes of the bivalve, that calculates water temperature, salinity, chlorophyll-a, inorganic nitrogen and phosphorous, organic nitrogen and phosphorous, COD and dissolved oxygen. We make one-dimensional calculations to clarify the seasonal variabilities in water qualities and nutrients cycle, and use a three-dimensional hydrodynamic model coupled with the ecological model to clarify the spatial distributions of water qualities. It is found that an increase of nutrient supply from the lower layer, caused by the intense vertical mixing, makes phytoplankton blooming active, and that the spatial distribution of the phytoplankton greatly depends on the habitat distribution of Corbicula Japonica. The calculation results for the nutrients cycle show that the amount of phosphorous consumed at primary production is more dependent on the biochemical and physical processes occurred in the lake than the inflow load supply. About 20% of primary production is ingested by Corbicula Japonica, and its purifying function is about 30% for COD. Because Corbicula Japonica stores nitrogen internally, the concentration of total nitrogen in the lake water is restrained and decreases in October in spite of the time of the maximum primary production.