The river basin approach of the Water Framework Directive (WFD) and the introduction of ecological status represent a shift in the assessment and management of freshwater systems from discipline-specific to more holistic, catchment-based principles. At the core of the WFD’s approach are catchments as highly interconnected systems. Despite strict timetables, progress towards achieving the WFD objectives has been slow, with deterioration in some cases not being halted. In this paper, looking at evidence from five European basins (Adige, Anglian, Ebro, Evrotas and Sava) we identify some of the key implementation challenges faced by each catchment during the development and implementation of the 1st River Basin Management Plans (RBMPs) of 2009. Despite significant differences in socio-ecological conditions, geographic coverage and starting points in the implementation between these river basins, findings highlight some similar key issues. The lack of a common systemic understanding of each river basin and detailed monitoring data to capture pressure-status interactions in order to anticipate how the system will react to interventions; as well as compliance driven implementation efforts were underlying problems in all five study areas. While some improvements to address these problems can be seen in the 2nd River Basin Management Planning Cycle (2015–2016), our findings demonstrate that a more effective approach is to question the deviation of the whole implementation from the directive’s systemic nature and therefore improve the adaptive, collaborative, participatory and interdisciplinary nature of the implementation efforts.