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Anthropogenic influence and natural processes exert important effects on the aquatic ecosystem of Sanya Bay in the northern part of the South China Sea. These effects result to the temporal and spatial differences of water quality in the bay. In this study, four-way principal component analysis is employed to identify the natural characteristics of the water in this bay, as well as the anthropogenic effects on its water quality. The results indicate that anthropogenic influence (nutrients as indicator) is the dominant factor that affects the water quality at the mouth of Sanya River (S1). This region exhibits the maximum effects of the discharge from Saya River, which is indicated by higher nutrient levels and Chl a than in outer bay. Both upwelling and mixing caused by monsoons are the dominant factors that affect water quality in the central and outer bays. The water exchange between the bay and open oceanic water exercises an important effect on the water quality in Sanya Bay. The information on the spatial and temporal variations of the water quality in Sanya Bay may be valuable for the socioeconomic development and human health in this area. [ABSTRACT FROM AUTHOR]