In order to achieve the objectives of the European Union's Water Framework Directive (WFD) for assessing chemical contamination of water bodies [i.e. checking compliance with Environmental Quality Standards (EQSs) for priority substances (PSs), and monitoring trends of contamination], it is necessary to propose reliable methodologies for monitoring micropollutants. For hydrophobic substances, this involves the use of integrative matrices (e.g., biota or sediment).We discuss here the implementation and the feasibility of a large-scale chemical biomonitoring approach for continental waters, considering the benefits and the limitations of existing biomonitoring strategies, the factors that can affect data interpretation, and the choice of species with regard to the WFD. Current scientific knowledge shows that, unlike the marine environment, continental waters have only a few established and standardized biomonitoring methodologies. From the literature reviewed, active approaches to biomonitoring (using transplanted organisms) appear to be more suitable than passive approaches (based on sampling of indigenous species), as they implement reproducible strategies, control biotic confounding factors and provide robust, comparable results. If fishes are organisms of choice for checking compliance with biota EQSs, they have several characteristics that limit their use for active biomonitoring, while macroinvertebrates represent a good compromise in terms of feasibility and fulfilling the objectives of the WFD