During a recent intervention in the Mondego River estuary, Portugal, the existing connection between the north and the more eutrophic south arm was enlarged, a nutrient-enriched freshwater input was diverted to the north arm and the remaining seagrass patches were protected from human activity. System restoration did not involve disruption of the sediment and successfully reduced the eutrophic state of the estuary. This provided an excellent opportunity to test a population-dynamics model of a common European estuarine bivalve, Scrobicularia plana, (da Costa, 1778) before and after the intervention. The model simulated the number of individuals in three different sampling stations, before and after system restoration, and is regulated by water temperature, salinity and population density. Our analysis indicated that the occurrence of extreme values of the environmental variables has the strongest effect on the model response and possibly on the real system. The model was calibrated and validated with independent data sets and the model performance was highest under the conditions after the management. This corroborates the notion that system restoration was successful and indicates that the system became more predictable after management.