Larval dispersal and connectivity are key processes that drive marine metapopulation dynamics, and therefore should be well characterized when designing effective management strategies. While temperature and food availability can structure marine species connectivity patterns, their relative contribution has not been thoroughly investigated in highly fragmented archipelagos. We used biophysical modeling of larval dispersal to explore the connectivity patterns of species with complex life-cycles across French Polynesia (FP), a territory formed by more than a hundred small, geographically isolated islands covering an area as large as Europe. We first simulated ten years of larval dispersal to investigate the spatial and temporal (seasonal and interannual) variability in larval dispersal pathways for different hypothetical species exhibiting a range of Larval Precompetency Period (LPP) values. Then, using the black-lip pearl oyster (Pinctada margaritifera) as a model species, we accounted for variability in the LPP induced by temperature and food availability, as derived from a Dynamic Energy Budget (DEB) model. The model showed that food availability and meso-scale turbulence (eddies) in the Marquesas jointly constrained larval dispersal, reducing its potential connectivity with other archipelagos in FP. However, accounting for food and temperature effects on larval development, barely changed the connectivity pattern at regional scale due to the remoteness of this archipelago. The DEB simulations further revealed seasonal and interannual variability in connectivity driven by environmental conditions. Our results highlight the importance of considering temperature and food in biophysical models to adequately capture dispersal, connectivity and to identify appropriate management units at the regional scale.