The implementation of the Water Framework Directive drew attention of water monitoring from the water quality to the ecological quality of aquatic ecosystems. Anthropogenic stressors affecting freshwater ecosystems are considered in wider scope than those predominantly focused on organic pollution, toxic pollution and eutrophication. Hydromorphological surveys are used for definition of reference conditions, identification of heavily modified water bodies, development of typology of water bodies, setting the most efficient sampling designs and for development and calibration of assessment systems based on biological quality elements. Decreasing impairment of running waters by organic pollution allowed to focus on the effect of hydromorphological degradation. The research team of Masaryk University in Brno participates in the projects funded by the 5th Framework programme of EU providing scientific support to the Water Framework Directive implementation. The results are mostly related to development and testing of the complex assessment systems in the conditions existing in the Czech Republic. The linkages between hydromorphological characteristics and biota of a lowland river are studied within the EURO-LIMPACS project.