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The European Union Water Framework Directive (EU WFD) demands from the EU member states to develop ecological assessment tools for lakes, streams and coastal/transitional waters. Assessment results then can be taken to decide about appropriate restoration measures in order to achieve a good ecological status of all natural surface water bodies. The ecological assessment is based on Biological Quality Elements (BQEs), ie phytoplankton, macrophytes/phytobenthos, fish and benthic invertebrates. While the trophic status of many lakes has been substantially improved in the last decades, recent studies (Brauns et al. 2007, Strayer & Findlay 2010) have pointed out the importance of littoral zones to lakes, and the ecological effects of hydromorphological degradation. Since macrozoobenthos communities of the eulittoral zone of lakes are sensitive to hydromorphological degradation (Brauns et al. 2007), their functional and taxonomic community composition is a suitable indicator for this environmental stressor. Hence in the WISER WP 3.3 we developed multimetric indices for several European biogeographic regions that may be used to assess hydromorphological lake shore alterations based on benthic macroinvertebrate surveys.