Before 2001, the ecological protection area in the Kenting National Park (KTNP), southern Taiwan, was poorly described. In this study, a set of four-year data (2001-2004) of seawater qualities at 19 sampling sites around the Nanwan Bay in the KTNP was used to explore anthropogenic impacts to ecological environment, especially coral reefs. The parameters of water quality were analyzed immediately after collection. The results showed that higher values of nutrients and suspended solids were attributed to the higher run-off around Nanwan Bay. The fluxes of nutrients and suspended solids were consistently correlated to rainfall. Hence, equations were developed to calculate nutrient fluxes and suspended solids by using only rainfall data. Our results show that suspended solids and ammonia were the dominant factors leading to the drop in coral coverage. In summary, the water quality in the intertidal zone of Nanwan Bay has been degraded and required greater attention.