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The population in the protected area for water supply has obvious influence to water resource protection, and environmental problems related to population factor should not be neglected. The article studied the environmental problems in the protected area for water supply of Yunlong Reservoir of Kunming City by means of field work, statistics analysis, forecast analysis, quantitative and qualitative analysis, etc. The result showed that the environmental problems in the study area were caused by both point and non-point source pollution. And the article forecast the life pollution load and non-point source pollution load based on the result of population development forecast. These ways, which included optimizing and adjusting agricultural structure in the study area, dealing with life domestic waste, controlling pollution and reducing agricultural non-point source pollution, enforcing migration and relocation, promoting the manpower development, setting up the ecological compensation mechanism etc, were proposed to become the countermeasures to resolve environmental problems in the study area.