This paper examines the challenges and policy imperatives involved in implementing the Polluter Pays principle (PPP) in the context of the Water Framework Directive (WFD). It presents the state of play of the Polluter Pays principle in EU Member States. It also analyses the coherence with other policies in EU Member States, such as agriculture, land planning and industry. Furthermore, it examines the practical limitations of the Polluter Pays principle in relation to diffuse and legacy pollution. Finally, it questions how the principle fits into the Green Deal and future water-related challenges in the EU. This is the second in a sub-set of four working papers within the Environment Working Paper series destined to support the further implementation of the economic pillar of the Water Framework Directive. The four papers are best read in combination and provide lessons which are relevant beyond the European Union.