The tailwater of ion-type rare earth mines in southern Jiangxi has caused serious water pollution problems in small watersheds. In this study, seven physical and chemical indicators, namely, pH, TOC, dissolved oxygen, ammonia nitrogen, nitrate-nitrogen, salinity, redox potential were selected and spatial interpolation, principal component analysis, and geographic detector methods, were used to quantitatively analyze and evaluate the spatial heterogeneity of water quality in the small watersheds in this region. Tailwater pollution in the whole basin of the study area is serious. The spatial difference is manifested as east tributary > mainstream and reservoir area > southern tributary. Source pollution is the smallest, and water quality pollution is mainly manifested by excessive ammonia nitrogen, salinity, and TOC. The spatial differences in the physical and chemical properties of water bodies are significant. The distribution of ammonia nitrogen content is consistent with the spatial distribution of soil and water pollution, while nitrate-nitrogen is the opposite. Other indicators also show a certain spatial regularity, and the spatial regularity of dissolved oxygen content is not obvious. Water pollution in mining areas is mainly due to a large amount of ammonia nitrogen ions remaining in the mountains. As a result, the southern tributary ecological pool has an obvious purification effect on water quality. Salinity is extremely affected by ammonia nitrogen and TOC, oxidation-reduction potential is affected by pH and TOC, and TOC is influenced by ammonia nitrogen and pH. Salinity, ammonia nitrogen, and TOC are the potential risk factors of major pollution. The changes in the physical and chemical properties of the pollution index are not independent of each other. From the perspective of macro and micro, the comprehensive water pollution assessment system is adopted to provide a new idea for the prevention and control of rare earth industry tail water pollution, and further make exploratory efforts for the study of industrial wastewater pollution.