Urban agglomerations are a primary spatial focus of socioeconomic activity and inherently include large volumes of embodied water. We have applied the concept of water metabolism health to comprehensively evaluate the overall operation of water systems in urban agglomerations and propose an innovative assessment framework. In particular, we constructed a water metabolism network (WMN) model to simulate a water system in which different cities and sectors are integrated, combining a newly compiled multiregional input-output (MRIO) table of water flow with ecological network analysis (ENA). A case study considering the Pearl River Delta (PRD) urban agglomeration in 2015 demonstrates that its network is well synergic but highly dependent, with considerable negative effects. Highly developed cities in southeastern of the PRD exhibit higher embodied water productivity and robustness but impose considerable negative effects on the water system. We found the agricultural sector to be a dominant controller of the network; the construction and service sectors represent the primary beneficiaries with strong competition. We suggest measures at various scales to improve water utilization efficiency and promote positive interactions between components, thus improving water metabolism system health for urban agglomerations.