Seasonal and annual variation of water qualities in the Shihwa Lake were observed from June 1996 to November 2002. We studied at the station of the upper streams and near the water gate of lake. After the flow of thw outer seawater through the water gate, the surface salinity in Shihwa Lake increased to the range of 25-30psu in both stations after October 1998. Due to the declination of the salinity differences between the surface and bottom water, the pycnocline in which had existed until 1997 has weakened, and made the water colimn mix vertically. This led to the improvement of anoxic/hypoxic environment at bottom waters after April 1998. However, despite the continuous flow of the outer seawater, the concentrations of chlorophyll-a at surface layer were varied from 2ug/L to 60ug/L, and these values indicated the eutrophication. The following organic matter load was greatly influencing the surface layer,s COD concentration. During the rainy season, the salinity at the surface layer fell below 15psu resulting in stratification between the surface and bottom layer. Organic matters that aere provided from the surface layer to the bottom layer due to active primary production in the year exhausted DO at the bottom layer, and the bulks of organic matters at bottom gave rise to hypoxic or anoxic environment. It was observed that the enrichment of ammonia and phosphate were main fators to worsen the water quality of the Shihwa Lake. The results of examining the annual variations in Shihwa Lake through principal component analysis shown that water characteristics in the rainy season were similar with those before input of outer seawater.