Based on a survey by means of questionnaires 37 methods were compiled that are used for the biological water quality assessment in running waters of the Danube River Basin. The assessment methods of the countries are described and analysed in terms of their approaches and possible steps towards harmonization are discussed. While some countries have based their water quality classification on different kinds of biotic indices other countries are developing integrated ecological assessment systems in line with the requirements of the EU Water Framework Directive (WFD). Until now the focus of biological water quality assessment has been on the assessment of organic pollution. In 13 out of 18 countries the Saprobic System is being used, but different modifications have evolved. Differences are due to the use of different indicator groups (benthic invertebrates, phytobenthos, and plankton), different saprobic indicator lists as well as different calculation methods. Besides adaptation to the requirements of the WFD a detailed approach for harmonization needs to be developed. This study constitutes preliminary steps towards harmonization of ecological quality assessment in the Danube River Basin.