As directed by the EU Water Framework Directive (WFD), all EU Member States are committed to achieve qualitatively and quantitatively good status water. To achieve this, countries need to monitor the chemical quality of their surface waters alongside the functioning of the aquatic ecosystems. With this in mind, the Rebecca initiative investigated the links between the chemical and ecological status of surface waters and the impact of different pressures. The consortium also aimed to develop tools that EU member countries could utilise for monitoring water and designing measures according to the WFD requirements. As a first step, project members collected chemical and biological data from different geographical regions in order to associate ecological thresholds with different water quality classes. These data sets were also used to investigate the relationship between various environmental effects and water quality. Phytoplankton was among the elements examined thoroughly as it is considered to be a promising indicator of healthy development of aquatic ecosystems. Additional indicators were assessed that could integrate the effect of combined pressures on lakes, rivers and coastal waters. These integrated indicators of the Rebecca project could provide valuable insight into the functioning of aquatic ecosystems and at the same time act as supporting tools for WFD implementation. Communication of project findings to the respective authorities and policymakers is expected to improve the quality of surface waters across Europe with obvious environmental benefits.