The recent discovery of Pacific oyster Crassostrea gigas (also known as Magallana gigas) spatfields in a Mediterranean lagoon intensely exploited for shellfish farming (Thau lagoon) revealed significant contrasts in spatial patterns of recruitment. We evaluated the processes that drive spatial patterns in oyster recruitment by comparing observed recruitment, simulated hydrodynamic connectivity and ecological variables. We hypothesized that spatial variability of recruitment depends on (1) hydrodynamic connectivity and (2) the ecology of the larval supply, settlement, metamorphosis, survival and biotic environmental parameters. We assessed recruitment at 6-8 experimental sites by larval sampling and spat collection inside and outside oyster farming areas and on an east-west gradient, from 2012-2014. Hydrodynamic connectivity was simulated using a numerical 3D transport model assessed with a Eulerian indicator. The supply of large umbo larvae did not differ significantly inside and outside oyster farming areas, whereas the supply of pediveligers to sites outside shellfish farms was structured by hydrodynamic connectivity. Inside shellfish farming zones, unfavorable conditions due to trophic competition with filter-feeders jeopardized their settlement. In this case, our results suggest loss of settlement competence by oyster larvae. This confirms our hypothesis of top-down trophic control by the oysters inside farming zones of Thau lagoon in summer that fails to meet the ecological requirements of these areas as oyster nurseries. Knowledge of oyster dispersal, connectivity and recruitment in coastal lagoons will help local development of sustainable natural spat collection. On a global scale, our method could be transposed to other basins or used for other species such as mussels, clams or scallops, to better understand the spatial patterns of bivalve recruitment. Management of the oyster industry based on natural spat collection will help develop a sustainable activity, based on locally adapted oyster strains but also by reducing the risks of transferring pathogens between basins and the global carbon footprint of this industry.