Water plays an essential role in social and economic sustainable development, and the relationship between socio-economic development and water resources sustainable utilization has been an important issue in water resources management. We aim to propose a water resources vulnerability assessment index with the dimensions of exposure, sensitivity and adaptability, and establish a water resources system model over the Pearl River Delta network river region based on the Vulnerability Scoping Diagram (VSD) framework and System Dynamics (SD) model. The city of Zhongshan, which is located in the Pearl River Delta is used as a case study. The vulnerability of the water resources in Zhongshan from 2021 to 2050 is simulated in four different scenarios (normal, technical innovation, social economic improvement, and comprehensive development models). The results showed that the vulnerability in all four scenarios span three grades in 30 years, including moderately vulnerable, slightly vulnerable, and not vulnerable. Among them, similar trends were found between scenarios 1 and 3, and between scenarios 2 and 4. Furthermore, the vulnerability level in scenarios 2 and 4 was lower than that in scenarios 1 and 3. The vulnerability of both scenarios 2 and 4 decreased first and then increased, with the average values of 24.64 and 27.63, respectively. Scenario 2 experienced 7 years of not vulnerable (2034 to 2040) and 23 years of slightly vulnerable (2021–2033, 204–2050), scenario 4 experienced 5 years of not vulnerable (2032–2036), 21 years of slightly vulnerable (2021–2031, 2037–2046), and 4 years of moderately vulnerable (2047–2050). Although the vulnerability of scenario 4 was slightly worse than scenario 2, its adaptability to economic and social development, water resources, and water environment was much higher than scenario 2. Considering the extent of socio-economic development and the level of adaptability of the local water resources and water environment, the study concluded that the comprehensive development model is more suitable for cities in the network river area. In this scenario, sustainable water use and management can be made possible through policy regulation that encourages higher water efficiency, sewage reuse rate, and centralized sewage treatment rate.