This study identifies the current situation of water pollution in the rivers, reservoirs and coastal waters in the Guangdong-Hong Kong-Macao Greater Bay Area, and analyzes the issues about urban water-logging as well as the changes in water volume in rivers and estuaries. The water pollution in the Bay Area is mainly caused by the intensive population and industrial activities in large cities. The imperfect sewage treatment system and management strategies have exacerbated the pollution. Water quantity problems mainly derived from the excessive encroachment of ecological water. By summarizing the development experience of the international advanced Bay Area, including improving legislation, raising standards, limiting emissions, and protecting the ecological water environment, this study proposes the following countermeasures for further management of water environment in the Guangdong-Hong Kong-Macao Greater Bay Area: 1) improving water use efficiency and strengthening sewage treatment; 2) promoting the construction of sponge cities; 3) controlling cofferdams and improving ecological protection; 4) accelerating the transformation of social economy.