Water resource security directly or indirectly affects the development of society, economy, and the environment, and is of massive significance for regional sustainable development. This study addresses whether anthropogenic activities, especially from tourism, significantly affect the freshwater quality in Hainan Province, China. The freshwater quality in Hainan Province was generally good in 2012 to 2015 (at level II, GB3838-2002). Agriculture, fishery, animal husbandry, and chemical oxygen demand discharge mainly affect freshwater quality in the Nandu and Changhua rivers. Water quality in Wanquan River is more susceptible to tourism in comparison with the Nandu and Changhua rivers. DO content in the Wanquan River fluctuated greatly. It remains necessary to closely monitor negative changes in water quality due to increasing tourism, especially in Wanquan River and eastern Hainan Province. The developed radial basis function neural network shows that the changes in water quality are predicted accurately in comparison with experimental values in the present study. Our results suggested that current anthropogenic factors had a modest effect on water quality on Hainan Island, while tourism had a perceptible effect in eastern Hainan. Our findings provide a reference for the interplay of water quality, people's livelihood, and economic development (tourism and port construction) in Hainan Province.