The Mondego estuary (Portugal) suffered major changes in environmental quality due to eutrophication, however, in the late 1990 s a restoration project was implemented in order to return the system to its original condition. The main goal of this paper is to evaluate the ecosystem response to the restoration measures applied at three different levels: water quality, primary producers and primary consumers. In post-restoration period a clear decline was observed in dissolved inorganic nitrogen which was reflected in the gradual recovery of Zostera noltii and a concomitant decline in green macroalgae. Macrobenthic assemblages responded variably to the recovery process. In the seagrass bed and intermediate area, there was a large increase in total biomass, but in the eutrophic area species diversity increased. Despite improvement in the ecological status of the system, full recovery has not been achieved yet, possible due to hysteresis in the dynamics of this system.