Dams affect the natural flow regime by altering the magnitude, timing and frequency of high and low flows. Many river ecosystems impaired by dams are currently being restored. Restoration success is difficult to quantify and is often assessed by comparing the restored system to an unimpaired static ‘reference’ system. However, restoring a river to past environmental conditions and assessing restoration success by comparing it to a static situation neglects natural system dynamics and non-linear, adaptive system responses. With this modelling study we evaluate long-term changes in river morphology, morphodynamics, riparian vegetation cover and habitat suitability of two fish species and two types of wetland vegetation in a meandering gravel bed river after removal of an upstream dam and complete restoration of the natural flow regime. We assessed the ecological and hydromorphodynamic recovery of systems impaired by two different dam operating regimes and three different time periods the dam was present by comparing these to a dynamic undisturbed situation. Modelling results show that recovery potential depends on how much the system has been changed by the dam and the system state at the start of the restoration, rather than the duration of the pressure. Even if the conditions shortly after restoration are comparable to pre-disturbance conditions, there can still be a time-lag in the system response where the future state of the restored system continues to deviate from the undisturbed situation. When this happens, the system can develop into an alternative dynamic equilibrium where recovery becomes increasingly difficult. These results stress the importance of considering natural variability in restored systems as well as in reference systems, requiring detailed spatio-temporal monitoring to assess restoration effects.