In the European Union, the Water Framework Directive provides a roadmap for achieving good water status and sustainable water usage, and a framework for the information, types of analysis, and interventions required by the Member States. Lack of previous knowledge in, and understanding of, interdisciplinary approaches across European countries has led to applications of corrective measures that have yielded less than favourable results. The natural capital paradigm, the assessment and monitoring of the value of natural capital, has the potential to convey information on the use of water resources and improve the connection between implemented measures and changes in the status of the resources, thus enhancing the effectiveness of policy interventions. In this paper, we present the natural capital accounting methodology, adapted to the requirements of the Directive, and demonstrate its application in two European catchments. Using economic methods, the asset value of two ecosystem services was estimated and associated with changes in water status due to policy instruments. Findings demonstrate that the asset value of water for residential consumption and recreational purposes fluctuates from year to year, influenced by current and future uses. Consequently, managing authorities should consider both current and emerging pressures when designing interventions to manage water resource sustainably.