The EU Water Framework Directive has created research opportunities and challenges for water-quality managers and palaeolimnologists alike. Opportunities have arisen through increased attention to water-quality issues, and these in turn have led to enhanced funding for palaeolimnological research. Scientifi c challenges include identifying aquatic-system pressures, assessing risks, defi ning non-impacted reference conditions and developing new indicator and classifi cation systems. These challenges have provided the aquatic science research communities with a range of highly relevant and urgent research questions. Addressing these questions requires a collaborative, systematic, whole-catchment approach that, in addition to palaeolimnologists, involves modellers and scientists from other disciplines, water-quality managers, policy-makers and the general public.