The Water Framework Directive (WFD) has established the concept of ecological quality as a method to improve European Union (EU) surface and ground waters. Ecological quality status is based on the composition and abundance of different biological quality elements, including fish fauna, with the supporting elements of hydromorphology and chemical and physico-chemical parameters. Monitoring for fish for the WFD began in Ireland in 2007. In parallel, classification tools were developed or refined for each surface water type (lakes, rivers and transitional waters) and then intercalibrated in a cross-Europe exercise to ensure consistency across all EU states. The development and basic concepts of three WFD-compliant ecological classification tools for fish and the cross-Europe intercalibration exercise are described for rivers, lakes and transitional waters.