Human activities and natural processes like mixing and/or upwelling driven by climate change have a strong influence on water quality in the coastal regions. Human activities are the dominant factor for water quality in the mouth of the Sanya River. This region exhibited the maximum influence of discharge from the Saya estimated by higher nutrient levels and chlorophyll a (Chl a). Natural processes are the dominant factor regarding water quality in outer bay. Both human activities and natural processes play important roles on water quality in Sanya Bay. Each hydrologic and ecological zone has a specific water quality response associated with the relative importance of both human activities and natural processes. Therefore, the information would be useful for regional agencies in developing a strategy to carry out scientific plans for resource use based on marine system functions.