For some decades, the Mondego estuary has been under severe ecological stress, mainly caused by eutrophication. The most visible effect was the occurrence of macroalgal blooms and the concomitant decrease of the area occupied by Zostera noltii beds. Since the end of 1998, mitigation measures were implemented in the estuary to promote the recovery of the seagrass beds and the entire surrounding environment. The present study offers a unique opportunity to evaluate the impact of disturbance and the success of the initial recovery process (before and after implementation of the management measures), over a 10-year period, having secondary production as the descriptor. Before the implementation of the mitigation measures, in parallel with the decrease of the Z. noltii beds, species richness, mean biomass and production also decreased, lowering the carrying capacity of the whole Mondego's south arm. Yet, after the introduction of management measures, the seagrass bed seemed to recover. Consequently, the biomass and production also increased substantially, for the whole intertidal area. Nevertheless, even after the mitigation measures implementation, natural-induced stressors, such as strong flood events induced a drastic reduction of annual production, not seen before the implementation of those measures. This shows that the resilience of the populations may have been lowered by a prior disturbance history (eutrophication) and consequent interactions of multiple stressors.