Large ships, particularly container ships, tankers, bulk carriers and cruise ships are significant individual contributors to air pollution. The European Environment Agency recognizes that air pollution in Europe is a local, regional and transborder problem caused by the emission of specific pollutants, which either directly or through chemical reactions lead to negative impacts, such as damage to human health and ecosystems. In the Marine Strategy Framework Directive 2008/56/EC of the European Parliament emissions from ships are mentioned explicitly in the list of pressures and impacts that should be reduced or minimized to maintain or obtain a good ecological status. While SOx and NOx contribute mainly to ocean and soil acidification and climate change, PM (particularly ultrafine particles in the range of nanoparticles) has the potential to act more directly on human and ecosystem health. Thus, in terms of risk assessment, one of the most dangerous atmospheric aerosols for environmental and human health is in the size range of nanoparticles. To our knowledge, no study has been carried out on the effects of the fraction that ends up in the water column and to which aquatic and sediment-dwelling organisms are exposed. Therefore, an integrated environmental risk assessment of the effects of emissions from oceangoing ships including the aquatic compartment is necessary. Research should focus on the quantitative and qualitative determination of pollutant emissions from ships and their distribution and fate. This will include the in situ measurement of emissions in ships in order to derive realistic emission factors, and the application of atmospheric and oceanographic transportation and chemistry models.