With the rapid development of social economy in Zhuhai and Macao, the problem of water resources has become increasingly prominent. For the comprehensive development of Zhuhai-Macao region and the protection of water resources, the water resources carrying capacity of water-society-ecology complex system is analyzed under four scenarios based on system dynamics, namely, status quo, priority of economic development, priority of environmental protection and integrated development, and then the developing trend of comprehensive water resources carrying capacity of 2020-2030 is estimated under these scenarios. The results showed that the water resources carrying capacity of all scenarios in the forecast period shows an increasing trend, and the total water consumption in the integrated development scenario is lower than 684×106 m3 required by the strictest water resources management system in Guangdong Province, which is better than other scenarios overall. Zhuhai’s water supply to Macao is about 15% of the total water supply, economic development and population growth will lead to a gap in water supply and demand in Macao, and integrated development scenario can relieve the pressure on Zhuhai’s water supply. Analysis of the water use efficiency of each development model reveals that reducing industrial water use is beneficial to environmental protection, but will hinder economic development, whereas improving industrial water use efficiency and implementing water conservation measures can achieve a win-win situation for both environmental protection and economic development. The water intake of Zhuhai and Macao are interconnected, so the local water resources are under great pressure. Therefore, appropriate measures should be taken to improve the carrying capacity of water resources in this region.