The Water Framework Directive (WFD) is an ambitious piece of legislation focused on achieving good ecological status as defined by deviations from reference conditions. Achieving good ecological status depends on collaboration between stakeholders, scientists and the public. However, public participation is restricted to consultations about implementing measures to achieve good ecological status, not in the goal setting. There are multiple, competing interpretations of good ecological status. This study addresses two of the pillars of the WFD, good ecological status and public participation. We argue that these two pillars are currently at odds when defining reference conditions for surface waters, and it is unclear how they can work together in practice. We also contend that there is an intention in the WFD to integrate these two pillars, but there is no legal support for their connection. In a case study of a small boreal lake in Sweden, we show that local people possess a great deal of historical knowledge, which they use to conceptualize reference conditions. Their conceptualizations are compared with fish and water chemistry monitoring by the regulatory authority as well as paleolimnological reconstructions of water quality dating back to the beginning of the 20th century. The knowledge that the local people have corresponds to the historical data available for the lake, particularly with water clarity. We highlight the subjective nature of the concept of ‘undisturbed state’ to show that it varies depending on values, knowledge and perceptions of lay-people, scientists and relevant authorities. The subjectivity of the concept of undisturbed state promises to be a way of linking the two pillars of the WFD. ► The concepts of reference condition and undisturbed state are inherently subjective. ► More flexible definitions of reference conditions will facilitate WFD implementation. ► Successful WFD implementation is dependent on increased public participation. ► Lay and scientific knowledge can be in agreement about trends in water quality.