Policymakers and managers have a very different philosophy and approach to achieving healthy coastal and marine ecosystems than scientists. In this paper we discuss the evolution of the assessment of the chemical status in the aquatic environment and the growing rift between the political intention (precautionary principle) and scientific developments (adaptive and evidence-based management) in the context of the pitfalls and practicalities confronting the current Marine Strategy Framework Directive (MSFD). The conclusion is that policymakers and water managers should move with the times and take on board new techniques that scientists are using to assess chemical status and apply new scientific developments in assessment studies of the chemical status. These new techniques, such as bioassays, are cheaper than the classic approach of checking whether concentrations of certain individual priority compounds comply with permissible thresholds. Additionally, they give more insight into the real impacts of chemical compounds.