Southern Taiwan’s Kenting National Park is a popular retreating place for many domestic and international tourists, with increasing tourist numbers potentially over-burdening the coastal ecosystems. To better understand human impacts, a long-term ecological research program was initiated in 2001 to track water quality at 14 coral reef-abutting sites throughout the park since then. Extracting the data from this 20-year survey, we found that increasing in the nutrient levels during the summer rainy season, together with the drops in salinity led by freshwater inputs (land- & rainfall-derived), was the main impact to coral reef ecosystem of Kenting. Cluster analysis further confirmed the nutrient influx was mainly attributed to the local discharge outlets with dense of villages and hotels at upstream. Therefore, more efforts are needed to input to control tourist number, treat waste water discharge and strengthen land protection facilities.