Current approaches have failed to deliver a truly integrated management of the different elements of the urban water system, such as freshwater ecosystems, drinking water treatment plants, distribution networks, sewer systems and wastewater treatment plants. Because the different parts of urban water have not been well integrated, poor decisions have been made for society in general, leading to the misuse of water resources, the degradation of freshwater ecosystems and increased overall treatment costs. Some attempts to solve environmental issues have adopted the ecosystem services concept in a more integrated approach, however this has rarely strayed far away from pure policy, and has made little impact in on-the-ground operational matters. Here, we present an improved decision-making framework to integrate the management of urban water systems. This framework uses the ecosystem service concept in a practical way to make a better use of both financial and water resources, while continuing to preserve the environment.