Abstract The European Union, Water Framework Directive (WFD) requires monitoring of riverine fish fauna. When the WFD came into force in 2000, most of the EU member states did not have fish-based assessment methods compliant to WFD requirements. Therefore, the objectives of FAME (http://fame.boku.ac.at), a project under the fifth R&D Framework Programme of the European Commission were to develop, evaluate and implement a standardised fish-based method for assessing the ecological status of European running waters. This paper synthesises the outputs of FAME and defines future research needs. Two different methodologies were used: the so-called spatially based modelling and the site-specific modelling, the latter leading to the European Fish Index (EFI). The advantage of the EFI is that, despite being a single index, it is applicable to a wide range of environmental conditions across Europe precluding the need for inter-calibration. The EFI will support the WFD towards harmonised/standardised assessment and management of running waters in Europe, thus enabling comparative analyses of the ecological status of running waters across Europe.