The Water Framework Directive (WFD) aims at improving the ecological status of waters. One of its basic principles of is to consider that in the absence of any human disturbance, each water body would reach a reference condition, which also means that re-establishing previous disturbance regime or abiotic conditions is enough to guide the recovery of biological communities. Nevertheless, a continuous change of large scale environment conditions, such as global warming, could lead to a definitive shift of aquatic ecosystems towards new stability domains. At the moment, it is still not demonstrated that within the timeframe of WFD implementation (i.e. up to 2027), an anthropogenic climate change signal will be observable above natural variability or adequately distinguishable from other human pressures at a level to cause major changes in ecological status. In case of a significant but slight change, we can expect modification of the community structures and function which could lead to a shift in reference condition. The associated consequences in terms of water body classification could be evaluated through a long-term monitoring network of reference sites and the use of model-based assessment tools. In such a perspective, a better understanding of uncertainties associated with ecological assessment and interactions between climatic conditions and local human pressures on aquatic environment are needed.