Background The municipality of Varese Ligure is a large, but sparsely populated territory; there are only about 2 400 inhabitants spread among more than 20 hamlets. The main settlements are the villages of Varese Ligure and San Pietro Vara. Due to the high number of hamlets and related economic costs, the area is not completely served by a public sewer system. Varese Ligure has two activated sludge-treatment plants, neither covering the disinfection stage. There are some Imhoff septic tanks and some private plants; there are also old houses whose sewers do not comply with modern standards. Water sources in rural areas receive effluents deriving from human activities as well as acting as a drinking-water resource. It is therefore essential that the exploitation of water resources and the impact of human settlements on natural water bodies are dealt with in a very careful, eco-compatible way. Objectives The main objective of the ECOMAWARU project was to achieve the requalification of water bodies in the Varese Ligure region as of “good ecological status” under the Water Framework Directive (2000/60/CE). The project aimed to develop and implement a water/wastewater management model in rural areas based on the phytodepuration technique, which uses microalgae as a tertiary treatment system; and to build two treatment plants of different sizes in an urban and a rural area to demonstrate the process, with a view to transferring the technology to other locations. Results The ECOMAWARU project demonstrated the performance of a prototype phytodepuration system with microalgae, in terms of feasibility, reliability and efficiency. This contributes to the project’s objective of improving water quality in water bodies in the Varese Ligure municipality region, through the sanitisation of point or cluster discharges. Phytodepuration is the reduction of contaminants in wastewater treatments by means of biological processes driven by aquatic photosynthetic organisms, in this case the project’s main innovation is to use microalgae in this context. The process is sustainable regarding energy consumption and management. The project constructed two prototype plants (photobioreactors) with microalgae: a closed bioreactor and an open one (pond). In an urban catchment area, a photobioreactor was installed at the outlet section of a settler, at the civil sewage treatment facility of Varese Ligure, to treat a portion of the wastewater flow; while in a rural area (the hamlet of Teviggio), a pond with microalgae was installed at the outlet section of an Imhoff tank to treat the entire wastewater flow. These were testing and extensively monitored, with the results published in a technical handbook on the phytodepuration technique. The project developed and implemented a comprehensive database, including biomass characteristics, the quality (chemical and physical parameters) of storm water and wastewater influent and effluent in the area of Varese Ligure area. Quality-performance indices were used to assess the photobioreactor plants’ performance. A GIS platform was also implemented, concerning the management of water and wastewater in the municipality of Varese Ligure. The aim was for the prototypes to abate 40-50% of the nutrient loads that would otherwise be discharged. The data obtained during the project’s lifetime showed that both the closed and open photobioreactor with microalgae, adopted as a tertiary treatment for wastewater, revealed excellent performance in terms of nutrient removal. A procedure was therefore defined for the recovery and reuse of this as biomass. Drawing on its findings, the project drafted a technical manual for the design, construction and management of microalgae phytodepuration systems. It also drafted a proposal regarding the adoption of the phytodepuration techniques, which was included in the Municipal Building Regulation of Varese Ligure. The project therefore provided a knowledge base for integrating phytodepuration into local regulations, in order to support the spread of green technologies, for example, in integrated water cycle management. This can potentially bring benefits in terms of people’s health in buildings and in terms of general quality of life. The treatment of wastewater with microalgae in bioreactors brings a range of environmental benefits, including smaller treatment surface areas than required by phytodepuration systems with macrophytes (e.g. terrestrial plants); increased efficiency of CO2 photosynthetic conversion with respect to macrophytes; and the oxygenation of effluent discharges into receiving water bodies. Long-term environmental benefits in the territory of Varese Ligure could derive from the improvement in the quality of receiving water bodies. The implemented GIS platform will enable easier and more effective control of the authorisation procedures for private wastewater discharges. Support for the replication of the phytodepuration techniques will boost sustainable green techniques by ARPAL (Regional Agency for Environmental Protection) in the territory of the Liguria Region. Long-term economic benefits could be expected from the reduced operating and investment costs for nitrogen and phosphorus removal from wastewater; the economic return for high-value products from the produced algal biomass; savings on the purchase of chemicals required for the intensive production of algal biomass; and through the promotion of an innovative technology boosting the green economy. The project’s work helps the municipality implement the EU Water Framework Directive (60/2000/EC), through the assessment of the quality of surface water bodies to help achieve “good ecological status”. The ECOMAWARU techniques can be replicated in any European rural community, such as those not served by public sewer systems, but efficiency and feasibility is constrained in colder regions where microalgae activity is inhibited. Current legislation does not need to be amended to facilitate the diffusion of the phytodepuration with microalgae system.