Patterns of bivalve larvae dispersal in the deep Ahe atoll lagoon was studied by using a numerical 3D transport model (MARS3D) coupled with a vertical swimming sub-model, forced mainly by tide and wind-induced currents. The simulations were validated against observations of larval dispersal monitored several days throughout the lagoon. Connectivity matrices describing larval exchanges inside the lagoon were inferred. Larvae displayed a significant dispersal capacity at the lagoon scale, especially with dominant eastern winds. With southeastern winds, larvae mostly remained in their origin sector. The total export rate of the larvae, toward the ocean through the pass and shallow lagoon borders, was independent of the wind conditions, with 1% of the total concentration exported per day. However, the tide-driven currents efficiently flushed larvae in sectors close to the pass. Connectivity matrices suggest that the south and west sectors were more suitable for spat collecting and that central sectors would be efficient sanctuaries if genitors were accumulated. Highlights ► We model bivalve larvae dispersal in a deep atoll lagoon with a 3D transport model. ► We introduce a vertical swimming model to reproduce vertical migrations. ► Connectivity matrices describing larval exchanges in the lagoon were inferred. ► Larvae displayed a significant dispersal capacity at the lagoon scale. ► We identify suitable sectors for pearl oyster spat collectors and genitors sanctuary.