Nearshore habitats are essential for many marine fish species but are subject to anthropogenic stressors. Assessing the consequences of essential fish habitat degradation on population dynamics and productivity is challenging. We address this by focusing on a metapopulation of the common sole Solea solea, a high-value, exploited flatfish in the Eastern English Channel (EEC). Multidisciplinary data and expert knowledge were compiled to build feasible restoration scenarios for the availability of suitable habitat (measured in habitat surface extent) and chemical quality of juvenile habitats in the highly anthropized Seine estuary, the largest estuary and potentially a sole nursery area of primary interest in the EEC. Scenarios were simulated with a spatially structured life-cycle model to investigate the consequences of local restoration on restricted nursery habitats in the estuary. Restoring surface extent and habitat quality in the Seine estuary dramatically enhances spawning stock biomass (+18%) and fishery catches (+13%) in the EEC. Restoring habitat quality has a greater effect than restoring habitat surface. Because of the low connectivity between subpopulations of sole in the EEC, most of the local restoration benefits remain regional and affect the subpopulation that directly depends on the Seine nursery, with only moderate spread to the entire EEC. Our study emphasizes the utility of spatial simulation models for integrating multidisciplinary knowledge and assessing the consequences of local anthropogenic pressures at wider metapopulation scales. We provide a means of building robust methods to assess the benefits of nearshore habitat restoration for enhancing fish populations and fisheries and integrate habitat value into the sustainable management of exploited species.