An international workshop on marine integrated contaminant monitoring (ICON) was organised to test a framework on integrated environmental assessment and simultaneously assess the status of selected European marine areas. Biota and sediment were sampled in selected estuarine, inshore and offshore locations encompassing marine habitats from Iceland to the Spanish Mediterranean. The outcome of the ICON project is reported in this special issue as method-oriented papers addressing chemical analyses, PAH metabolites, oxidative stress, biotransformation, lysosomal membrane stability, genotoxicity, disease in fish, and sediment assessment, as well as papers assessing specific areas. This paper provides a background and introduction to the ICON project, by reviewing how effects of contaminants on marine organisms can be monitored and by describing strategies that have been employed to monitor and assess such effects. Through the ICON project we have demonstrated the use of an integrating framework and gleaned more knowledge than ever before in any single field campaign about the impacts contaminants may have in European marine areas.