The increasing global rate of urbanisation and concurrent global climate changes create new challenges and new opportunities for managing cities, water resources and related quality of life. In most strategies, however, water ecosystems, which are the fundamental component of the integrated urban water resources management (IUWRM), are regarded as objects of protection or rehabilitation; not, as postulated by ecohydrology, as management tools. This paper addresses the possibilities of: (i) the functional incorporation of aquatic ecosystems into the IUWRM; (ii) optimising their functioning by local ecohydrological approach; and (iii) integration of ecosystem functions on a city scale to build system solutions for more resilient cities. Two case studies of the UNESCO MAB/IHP demonstration network representing different urban development patterns are given. The City of Łodz´ (Poland) uses water-resource based urban retrofitting for improving the quality of life and attracting inhabitants, departing from the analysis of longitudinal dynamics of nutrient transition in the river–reservoirs system, towards proposing an alternative concept of spatial city development. The city of Lyon (France), with intensive periurban development and population growth, provides a hierarchy of stream reaches to cope with combined sewer overflows to help municipalities to better position future urban runoff outlets. This article envisions also the future management of urban waste and storm waters using urban rivers, assuming resilient cities will depend on the integrity of environmental, technical and spatial planning decisions. The virtues of ecohydrology are discussed in this respect.