Enhancing the resilience of water resource systems is an effective strategy for addressing the uncertainties posed by climate change and other shocks. Current research on water resource system resilience primarily focused on the system's ability to maintain regular service provision to socio-economic sectors during disturbances, often overlooking the capacity of these sectors to adapt to such disruptions. This paper defined water resource system resilience by considering the demand elasticity of socio-economic sectors for water resources and incorporated both physical and virtual water to analyze the dynamic resilience of urban agglomeration water systems under external disturbances. Based on the fulfillment of water demand under disturbances, resilience was categorized into three stages: Resistance, Adaptation, and Recovery, thereby establishing a theoretical RAR resilience assessment framework for urban agglomeration water resource systems. This framework allowed for dynamic resilience assessments from both the supply and demand perspectives. The Pearl River Delta urban agglomeration was used as a typical case study to apply the proposed approach. The results indicated that, over the past decade, the resilience of the water resource system in most cities within the Pearl River Delta gradually improved. Although ideal water demand was not fully met, it remained within a manageable elasticity range. Due to differences in urban water resource endowments and development stages, the contributions of physical and virtual water to the resilience of the water resource system varied. This integrated approach, combining both physical and virtual water demand, offered valuable insights to enhance resilience of water resource system in urban agglomeration and could help propose tailored resilience enhancement strategies for different cities.