Throughout the European Union (EU), high concentrations of nitrates and pesticides are among the major polluting components of drinking water and have potential long-term impacts on the environment and human health. Many research projects co-funded by the European Commission have been carried out, but the results often do not influence policy making and implementation to the extent that is duly justified. This paper assesses several issues and barriers that weaken the role of science in EU policy making and EU policy implementation in the case of agricultural impacts on drinking water quality. It then proposes improvements and solutions to strengthen the role of science in this process. The analysis is conceptual but supported empirically by a desk study, a workshop, and complementary individual interviews, mostly with representatives of organizations working at the EU level. The results indicate that perceived barriers are mostly observed on the national or regional level and are connected with a lack of political will, scarce instruction on the legislation implementation process, and a lack of funding opportunities for science to be included in policy making and further EU policy implementation. In response to that, we suggest translating scientific knowledge on technological, practical or environmental changes and using dissemination techniques for specific audiences and in local languages. Further, the relationship between data, information and decision making needs to change by implementing monitoring in real-time, which will allow for the quick adaptation of strategies. In addition, we suggest project clustering (science, policy, stakeholders, and citizens) to make science and research more connected to current policy challenges and stakeholder needs along with citizen involvement with an aim of establishing sustainable long-term relationships and communication flows.