With regard to the problems of prevention and control of rural water environment in Guangxi Zhuang Autonomous Region, the main pollution modes are summarized from four aspects of agricultural non- point source pollution, water pollution of township enterprises, life source pollution and inter-river basin pollution. The root causes for pollution are discussed from the perspectives of externality of water environment pollution, attribute of quasi-public goods of water resources and economic structure. Finally, on the basis of the existing control measures and results, some countermeasures and suggestions are put forward for the long-term effective management mechanism of rural water environment, including adjustment of industrial structure, market management and application of information technology.