Using ecological network analysis, we analyzed the network structure and ecological relationships in an urban water metabolic system. We developed an ecological network model for the system, and used Beijing as an example of analysis based on the model. We used network throughflow analysis to determine the flows among components, and measured both indirect and direct flows. Using a network utility matrix, we determined the relationships and degrees of mutualism among six compartments – 1) local environment, 2) rainwater collection, 3) industry, 4) agriculture, 5) domestic sector, and 6) wastewater recycling – which represent producer, consumer, and reducer trophic levels. The capacity of producers to provide water for Beijing decreased from 2003 to 2007, and consumer demand for water decreased due to decreasing industrial and agricultural demand; the recycling capacity of reducers also improved, decreasing the discharge pressure on the environment. The ecological relationships associated with the local environment or the wastewater recycling sector changed little from 2003 to 2007. From 2003 to 2005, the main changes in the ecological relationships among components of Beijing's water metabolic system mostly occurred between the local environment, the industrial and agricultural sectors, and the domestic sector, but by 2006 and 2007, the major change was between the local environment, the agricultural sector, and the industrial sector. The other ecological relationships did not change during the study period. Although Beijing's mutualism indices remained generally stable, the ecological relationships among compartments changed greatly. Our analysis revealed ways to further optimize this system and the relationships among compartments, thereby optimizing future urban water resources development.