The conflicting needs of water managers (i.e., quick relevant operational responses) and ecologists (i.e., time consuming in-depth research) have been noted in freshwater biomonitoring and exist even today. To contribute to solving this dilemma, we are proposing a novel biomonitoring approach, which among many others, could be successfully used in this field and further developed in the future. In this approach, 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, such as various biotic indices, and integrate the information given by individual biotic indices. Functional traits and calculation of an ecological potential in porous aquatic habitats, comprising 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 waters and groundwater. The objectives of ecological quality, ecological potentials and resilience capacity that need to be preserved or rehabilitated in aquatic habitats can be established. In lakes, a similar approach was followed and a general typology of lake functioning was proposed, including that for urban lakes and reservoirs. All those biomonitoring tools can be transferred to the end-users, but at the same time, these tools should be further researched and refined. Finally, this paper aims to promote practical high-tech tools, which are continually and interactively connected with the ongoing research.
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