This paper is the result of hydrogeological survey engineering. Objective Due to the dual impacts of climate change and human activities, there is an urgent need to deepen the understanding of the evolution of water resources in the Greater Bay Area of Guangdong, Hong Kong and Macao, with a view to providing a scientific basis and decision–making support for the realization of the sustainable management of regional water resources. Methods This paper employs a combination of qualitative and quantitative methods, leveraging in–depth analysis of historical literature alongside multi–source water resource monitoring data to comprehensively examine changes in hydrology, precipitation, land cover, and other environmental factors related to water resources in the Greater Bay Area over the past 40 years (1980–2020). It also explores the regional patterns of differentiation in these changes. Results Our findings reveal a general water resource distribution trend of "abundance in the west and north, scarcity in the east and south," with an average temperature of 22.2℃ and annual precipitation of 2022.1 mm from 1980 to 2022. The study observes a major cyclical change every 4.1 years. The average runoff of the Xijiang, Beijiang, and Dongjiang Rivers is quantified, alongside the variation in runoff coefficients, reflecting a warm and humid climatic trend. Concurrently, the total volume of water bodies exhibits a declining trajectory, while vegetation cover overall shows an increase but with local degradation. Conclusions The study identifies 41 potential emergency backup water sources, with a sustainable extraction capacity of 2342600 m³/day.It highlights the ongoing mismatch between water resources and economic development in the Greater Bay Area, the reduction of water ecosystem service functions, the spatial and temporal imbalances in water resource distribution, and the region's over–reliance on a predominantly surface water–based supply structure.