Marine and coastal ecosystems – and thus the benefits they create for humans – are subject to increasing pressures and competing usages. For this reason, the European Union (EU) adopted the Marine Strategy Framework Directive (MSFD), which is to guide future maritime policy in the EU and aims at achieving or maintaining a good environmental status (GES) of the European seas by 2020. To this end, the MSFD requires the development of improvement measures, which have to be assessed inter alia by examining their cost-effectiveness and by carrying out cost-benefit analysis (CBA) before their implementation. In this paper, we investigate the applicability of environmental CBA in the marine context and identify and discuss problems that may hamper the environmental effectiveness of the MSFD. For example, marine ecosystem services are much less tangible than terrestrial ecosystem services. This implies greater challenges for the quantification of societal benefits in a marine context. One finding is that the limitations of environmental valuation methods regarding their ability to capture the whole total economic value of improvement measures are a potential source of problems, as the MSFD allows countries to disregard measures with disproportionately high costs. The trans-boundary nature of the main European seas adds to the complexity of the valuation task, e.g. due to the danger that benefits that occur outside of national territories are neglected. Moreover, the current state of knowledge on the functioning of complex marine ecosystems and the links to socio-economic impacts and human well-being seems insufficient to meet the MSFD requirements.