Background Four Natura 2000 sites are located within the Mølleåen river system situated just north of Copenhagen (Denmark). These unique sites are of regional, national and European importance: the river system contains 16 Annex I Habitat Directive listed species, of which five are prioritised by the Community, and six Annex II and/or IV species. However, the conservation status for several habitat types and species of Community importance is considered unfavourable or uncertain. The natural water flow level in the river system has been greatly reduced, mainly due to water extraction for drinking purposes and a reduced influx of rainwater due to urbanisation in the catchment area. Insufficient water flow and reduced water quality directly impacts a range of habitat types and species. Objectives The main objective of the REFLOW project was to contribute to a favourable conservation status of European river systems, by demonstrating how to re-establish a natural water flow level by transporting treated wastewater back into the river ecosystem. The aim of this demonstration project was to implement a concerted conservation action plan to restore and maintain a favourable conservation status for selected habitat types and species in the four Natura 2000 sites within the Mølleåen river ecosystem in Denmark. The project also addressed the threats of eutrophication, watercourse modification, encroachment and biodiversity loss through specific conservation actions in localities with high conservation value. Results The REFLOW project restored watercourses in the upstream part of the Mølleåen river system (approximately 30% of the foreseen stretch), with direct and beneficial impacts on two Natura 2000 areas. The project reached its target of clearing around 15.8 ha of trees and scrub, and expanding grazing enclosures (13.4 ha), at two important localities (Klevads Mose and Vaserne). Although the project did not achieve many of its objectives during its LIFE time, the knowledge gained during the Environmental Impact Assessment (EIA) process has demonstrated that the project idea is still viable. The issuing of the EIA after the project finalisation means that the project’s remaining work programme can be implemented, and the beneficiary, municipalities and wastewater treatment plant in the area are strongly committed to doing so. REFLOW improved the conservation status of approximately 500 m of watercourses within the Habitats Directive type 3260 ‘water courses of plain to montane levels with the Ranunculion fluitantis and Callitricho-Batrachion vegetation’ and also developing towards a favourable conservation status several other habitat types, in particular 2.6 ha of 7140 ‘transition mires and quaking bogs’, 0.5 ha of 7220* ‘petrifying springs’, 1.1 ha of 7230 ‘alkaline fens’, and an area of 6230 ‘species-rich Nardus grass lands’. The project has probably also improved the conservation status of three annex-listed species: Triturus cristatus cristatus, Leucorrhina pectoralis and Vertigo moulinsiana. The project team built a pipeline to Kalvemosen and 200 l/s of sufficiently treated wastewater is now being lead to Kalvemosen, and further via Kirkeskov bæk. Methodology developed during the project is being used to restore Lakes Vejle and Søllerød, while Lake Furesø remains in a good ecological condition. However, the project was unable, as foreseen, to demonstrate an approach to integrated nature and environmental management using an innovative cost-efficient method to improve the water quality in the degraded river system. Nevertheless, the beneficiary and cooperating partners have demonstrated the feasibility of cleaning wastewater to a degree that would allow it to be returned to river systems of good ecological quality. Through modelling, the beneficiary has demonstrated that this can be done within the objectives of the Habitats Directive and the Water Framework Directive (WFD). Advanced wastewater treatment methodology implemented at the WWTP Mølleåværket will certainly have a demonstration value (though it was not developed through the LIFE project as such), with good potential for replication in other areas. Knowledge on immobilisation of sediment-phosphorous gained by the project also has a demonstration value, although the theoretical results need to be underpinned by practical implementation of the measures. The project increased public awareness and support for conservation actions in Natura 2000 network sites in the river system. The two restored Natura 2000 open grassland areas, as well as the restored stretch of watercourse, in the Greater Copenhagen area are intensively used for recreation and have a high landscape value. The project’s restoration actions in both areas have enhanced them for recreation and visitors. REFLOW’s objective of restoring Lake Vejle, Lake Søllerød and Kirkeskov bæk will depend on the beneficiary being allowed to implement its proposed measures. The EIA permit is in place, but it has been appealed and a final decision will be taken by the Environmental Appeal Board. The waterflow of the lower part of river Mølleå has been restored to close to natural conditions and is developing towards a favourable conservation status. This approach, of returning treated wastewater to enhance water flows, is now being implemented in other EU rivers.