To contribute to solving the dilemma of the conflicting needs of water managers and ecologists, we are proposing an approach for the use and development of existing biomonitoring tools. For running waters, a harmonization system allows to use a set of various biotic indices. Functional traits are regarded as a basis for assessing ecological functioning. They take into account the dynamics of water exchanges between surface water and groundwater. In lakes, the oligochaete index IOBL describes the metabolic potential of deep-water sediments. Coupled with percent pollution-sensitive oligochaete species, it allows to defi ne a typology of lake sediments. The presented tools are integrated through a conceptual framework, including research management and technology transfer procedures.