In the Water Framework Directive (WFD), ‘water quality’ now refers to a comprehensive assessment of the state of aquatic ecosystems (whether fluvial or lacustrine), which are evaluated by their deviation from a pre-determined historically-based reference condition. However, the WFD does not consider theoretically whether water quality can be expected to recover to a historical condition; it simply assumes that it is possible for quality to be reversed. The main aim of this paper is to ask, in the particular case of the river system, whether its quality is practically reversible or not. By examining empirical evidence and external stresses, we argue that river water quality is more likely to be irreversible. Consequently, there is a dilemma: historical reference states are insufficient if river water quality is irreversible, but a clear quality management goal is needed. To resolve this problem, we suggest that future monitoring practice may need to pay more attention to the river aquatic ecosystem dynamics.