Water resources security is a major event involving long-term national security and a prerequisite for ensuring the high-level implementation of major national strategies in the Guangdong-Hong Kong-Macao Greater Bay Area. The special regional conditions and water conditions make the new and old water issues in the Guangdong，Hong Kong，Macao Greater Bay Area complicated and intertwined. Water security is facing serious challenges，and the water management system and mechanism are in urgent need of innovation. President Xi’s “Water Saving Priority，Spatial Balance，System Governance，Two-Handed Forces” Sixteen-character Water Management Policy and the General Keynote of Water Conservancy Development of “Water Conservancy Projects Compensating for Shortcomings and Strong Supervision in the Water Conservancy Industry” as the fundamental guide，focusing on the Guangdong-Hong Kong-Macao Greater Bay Water security issues in the district are centered on the most stringent water resources management system，water saving priority water treatment policy，river and lake length system，water resource property rights system，water ecological space management control degree，unified water resource allocation，water ecological compensation mechanism，and cooperative mechanisms and other aspects were explored and researched，and suggestions for innovation and implementation were put forward. By giving full play to the advantages of policy and system innovation，the system advantages can be better transformed into governance effectiveness. The related results can provide a reference for the advancement of water resources security in the Guangdong-Hong Kong-Macao Greater Bay Area to serve the construction of an ecological civilized society and high-quality development in the Guangdong-Hong Kong-Macao Greater Bay Area.