We examined the temperature records of Lake Biwa spanning more than 30 years to determine whether consistent long term changes exist. The bottom water temperature of Lake Biwa has increased by 1.4°C over 33 years. Especially, the water temperature increased dramatically since 1980s. The rate of the interannual temperature increase between 1980 and 1996 was 0.08-0.12°C yr^-1. This rate differed according to the depth. It was high in the deep hypolimnion and highest just above the bottom (90 m). The inclease of the water temperature was caused by the warming of the climate. The variation of the bottom water temperature is similar to that of the air temperature in winter. Using a one dimensional diffusion model, we show that the difference in the rate of the temperature increase with depth was caused by the fact that the interannual increase of the air temperature was more rapid in winter than in summer. The rapid increase of the bottom water temperature was caused by the mild winter cooling. If the winter climate becomes warmer so rapidly that the complete mixing cannot, occur in winter, the bottom water stagnates interannually and causes the hypoxia of the bottom water.