The Water Framework Directive 2000/60/EC (WFD) is widely accepted as the most substantial and ambitious piece of European environmental legislation to date. It has been referred to as a once in a generation opportunity to restore Europe's waters and a potential template for future environmental regulations. However, fifteen years since it was adopted, and with many problems and delays in its implementation, the WFD has not delivered its main objectives of non-deterioration of water status and the achievement of good status for all EU waters. Putting aside the daunting technical and organisational challenges of its implementation, this paper aims to shed light on why the great expectations that came with the WFD have not yet been fully realised. It reviews how the Directive has been interpreted, focusing on its intentions and how they were applied. The findings reveal the absence of the paradigm shift towards the systems (integrated) thinking that the WFD was grounded on, as a fundamental problem with its implementation. This is also evident in cases where the Directive has been criticised as a policy tool or when implementation efforts were reviewed, indicating misunderstandings even of its core principles. This inherent departure from the Directive's systemic intention and methodological approach needs further investigation, as it could be the reason behind many of its problems and delays. Unless current implementation efforts are reviewed or revised in light of this, enabling the paradigm shift required to ensure a more sustainable and holistic approach to water management, the fading aspirations of the initial great expectations that came with the Directive could disappear for good. Display omitted •Systems thinking is a pre-requisite to effective WFD implementation.•Departure of implementation efforts from the WFD's intention identified.•Misunderstandings even of WFD core principles highlighted•Implementing the WFD like any other directive will not work.•Acknowledging the WFD's systemic intent is required to deliver its full potential.