<jats:title>Abstract</jats:title> <jats:p> Marine protected area (MPA) networks are important for supporting biodiversity, enhancing ecosystem resilience, and facilitating species recovery. For the effectiveness of conservation and restoration, functional connectivity plays a vital role. The dispersal, movement, and successful establishment of organisms between suitable habitats and MPAs ensure long‐term sustainability of the populations. Despite its importance, functional connectivity is rarely integrated into restoration planning, which limits the effectiveness of species reintroductions, habitat connectivity, and adaptation to environmental changes. In this study, we applied an integrative approach combining molecular detections (environmental DNA [eDNA] and meroplankton metabarcoding) with biophysical modeling to explore the functional connectivity between two Natura 2000 MPAs in the North Sea: Borkum Reef Ground (BRG) and Sylt Outer Reef (SOR). We focused on the European flat oyster ( <jats:italic>Ostrea edulis</jats:italic> ), a reef‐building species that once provided vast reef habitats but is now functionally extinct in the German Bight and is therefore the subject of recent restoration measures at BRG. Our results showed partial but informative correspondence between molecular detections of oyster genetic traces and the modeled larval pathways during the June–July 2022 sampling period. We further explored larval dispersal across entire spawning seasons in 2022 and 2023. Connectivity between BRG and SOR was highly dependent on larval drift depth. Surface‐drifting larvae showed strong interannual variability, with 3% reaching SOR in 2022 when northwesterly winds dominated, increasing to 22% in 2023 under westerly and southwesterly winds. Larvae drifting at depth, however, exhibited near‐zero connectivity, leading to high self‐recruitment rates, with over 25% settling near the original restoration sites. Our results demonstrate that wind‐driven currents are a key driver of interannual variability in larval retention and dispersal. Additionally, they highlight the role of biological traits, such as vertical positioning and pelagic larval duration, in shaping connectivity between MPAs and oyster restoration sites. These findings emphasize the need to integrate connectivity assessments into MPA management and the restoration planning of reef‐building benthic species. The interdisciplinary approach presented here provides a quantitative framework for assessing connectivity under species‐ and site‐specific conditions, offering a transferable tool to evaluate the restoration potential of other species and enhance the functional network between MPAs. </jats:p>