The innovative approach to the protection and management of water resources at the basin scale introduced by the European Union water framework directive (WFD) requires new scientific tools. WFD implementation also requires the participation of many stakeholders (administrators, farmers and citizens) with the aim of improving the quality of river waters and basin ecosystems through cooperative planning. This approach encompasses different issues, such as agro-ecology, land use planning and water management. This paper presents the results of a methodology suggested for implementing the WFD in the case of the Seveso river contract in Italy, one of the recent WFD applications. The Seveso basin in the Lombardy region has been one of the most rapidly urbanizing areas in Italy over the last 50 years. First, land use changes in the last 50 years are assessed with the use of historical aerial photos. Then, elements of an ecological network along the river corridor are outlined, and different scenarios for enhancing existing ecological connections are assessed using indicators from graph theory. These scenarios were discussed in technical workshops with involved stakeholders of the river contract. The results show a damaged rural landscape, where urbanization processes have decimated the system of linear green features (hedges/rows). Progressive reconnections of some of the identified network nodes may significantly increase the connectivity and circuitry of the study area.