Abstract: The construction of the Guangdong-Hong Kong-Macao Greater Bay Area (the GBA) is a national-level strategy. In the context of ‘one country, two systems and three jurisdictions’, more requirements are put forward for the connection of rules and mechanisms in the GBA. At present, the GBA is faced with the problem of disunity of eco-environment standards. A unified and coordinated eco-environment standard system has not been formed in the region. To strengthen cooperation on eco-environmental protection and promote convergence of eco-environment standards in the GBA is of great significance to promoting joint environmental prevention and management in the region and jointly building a beautiful Bay Area. This paper compared and analyzed the current water environmental quality standards and water pollutant discharge standards in Guangdong, Hong Kong and Macao (Hong Kong-Macao-Pearl River Delta Region). In addition, combined with the experience of water environment standards in the world-renowned Bay Area, suggestions for the implementation of water environment standards in the GBA were put forward. The results show that there are obvious differences in eco-environment standard systems in the GBA. The water environmental quality standards and water pollutant discharge standards among Guangdong, Hong Kong and Macao are significantly different in terms of standard classification, control methods, evaluation indicators and limiting values. It is difficult to achieve comprehensive connection because some standard limiting values are not uniform. Based on its characteristics, it is recommended to establish a multi-dimensional cooperation mechanism for the standardization of the ecological environment, and gradually deepen the pilot project of the connection of the water environment standards in the GBA.