In the late summer of 1994, the water level of Lake Biwa was reached to 123cm under the standard level by the shortage of water. The level is the lowest since measurement of the water level was begun. This shortage of water was caused by small rainfall in the rainy season and high temperature from May to middle of September. The weather condition gave various influences to the water quality of the lake. But the results were different by shape of basins in the lake. In the deep and large northern basin, NO3-N, the only detectable nutrient, was disappeared from surface layer in early stage. It brought small amount of algae and high transparency in the basin. In the shallow and small southern basin, high concentrations of COD were measured, as retention time in the basin became long and the effect of influx from the northern basin was decreased. In the more shallow and half closed water area, Akanoi Bay, extremely high concentrations of total phosphorus were measured, it caused continuous generation of water bloom of blue-green algae under the weather condition.