The contradictory demands of managers (quick relevant operational responses) and ecologists (need time for in-depth research) involved in freshwater biomonitoring are still relevant today. To contribute to solving this dilemma, we are proposing a novel biomonitoring approach, which among many others, could be used in this field and further developed in the future. Biomonitoring actions are integrated in conceptual schemes, in which hydrology, chemistry, hydrogeology and geomorphology bear as much importance as biology. Among biomonitoring tools, a harmonization system allows end-users to use a set of qualitative indicators (various biotic indices) and integrate the information given by individual biotic indices. Functional traits and calculation of an ecological potential in porous aquatic habitats (surficial coarse sediments and the hyporheic system) are regarded as a basis for assessing ecological functioning of streams and rivers. This last methodology takes into account the dynamics of water exchanges between surface water and groundwater. Objectives of ecological quality, ecological potentials and resilience capacity that need to be preserved or rehabilitated in aquatic habitats are established. In lakes, a similar approach was followed and a general typology of lake functioning was proposed, including that for urban lakes. All those biomonitoring tools are transferred to end-users and subject to further research. The final purpose is to promote practical high-tech tools which are continually and interactively connected with ongoing research.