Differences in water quality standards in China and problems in implementation of these standards are systematically analyzed in this paper. The results show that various kinds of national water quality standards and industrial standards lack a connection and are not scientific. This leads to deviations and contradictions between standard limits. The current water resources quality standards established by the Ministry of Water Resources of China are not applicable to the protection of drinking water safety and evaluation of the present situation of water resources quality and pollutant discharge, and cannot meet the requirements of water resources protection at present in different water function zones of various water areas. Therefore, when revising the existing water resources quality standards, the administration departments should determine water environmental protection goals and strengthen coordination to build complete, scientific, and practical water quality standards.