Integrated assessment is a prominent issue in environmental research due to the Marine Strategy Framework Directive (MSFD) of the EU. Researchers from the Thünen institute work together with colleagues from national and international expert groups on the development of scientific concepts for the MSFD implementation. Integrated assesment means the inclusion of single parameters like contaminants, biomarkers or fish diseases in one number. Selection and weighting of the parameters as well as the treatment of "alarming" signals is a challenge.