The Water Framework Directive (2000/60/EC) is an innovative piece of legislation aimed at protecting the quality of all continental and coastal waters in Europe through an ecological evaluation of the ecosystems. Since it is widely acknowledged that the greater the ecological realism the greater the difficulty of its definition, we describe the different uses of benthic organisms as a tool for assessing the quality of sediment in lakes. We review the responses from single species to the community. We focus on studies in the laboratory and in the field, and we also critically consider the use of predictive models for these evaluations. Our discussion of the information collected underlines the importance of the relation between sensitivity of single species and contaminants. Moreover, the recent approach in developing mechanistic models to predict the response of natural communities seems to be particularly powerful for community ecology, and we strongly recommend more effort along these lines