Changes in larval import, export, and self‐seeding will affect the resilience of coral reef ecosystems. Climate change will alter the ocean currents that transport larvae and also increase sea surface temperatures (SST), hastening development, and shortening larval durations. Here, we use transport simulations to estimate future larval connectivity due to: (1) physical transport of larvae from altered circulation alone, and (2) the combined effects of altered currents plus physiological response to warming. Virtual larvae from islands throughout Micronesia were moved according to present‐day and future ocean circulation models. The Hybrid Coordinate Ocean Model (HYCOM) spanning 2004–2012 represented present‐day currents. For future currents, we altered HYCOM using analysis from the National Center for Atmospheric Research Community Earth System Model, version 1‐Biogeochemistry, Representative Concentration Pathway 8.5 experiment. Based on the NCAR model, regional SST is estimated to rise 2.74 °C which corresponds to a ~17% decline in larval duration for some taxa. This reduction was the basis for a separate set of simulations. Results predict an increase in self‐seeding in 100 years such that 62–76% of islands experienced increased self‐seeding, there was an average domainwide increase of ~1–3% points in self‐seeding, and increases of up to 25% points for several individual islands. When changed currents alone were considered, approximately half (i.e., random) of all island pairs experienced decreased connectivity but when reduced PLD was added as an effect, ~65% of connections were weakened. Orientation of archipelagos relative to currents determined the directional bias in connectivity changes. There was no universal relationship between climate change and connectivity applicable to all taxa and settings. Islands that presently export large numbers of larvae but that also maintain or enhance this role into the future should be the focus of conservation measures that promote long‐term resilience of larval supply.