Larval dispersal by ocean currents is crucial for many marine species’ life cycles, yet temporal variability in dispersal remains poorly understood. Using a 20-year timeseries of biophysical simulations, we model how dispersal variability can impact reef fishery populations. Even when metapopulations are fished at supposedly sustainable levels (40% unfished biomass), temporal variation in larval dispersal alone can drive up to a third of local populations below depleted thresholds. When metapopulations are depleted to 20% of unfished biomass, up to 60% of local populations drop below 10% unfished biomass, where key ecological functions are unlikely to be maintained. This risk is particularly acute in metapopulations where larval settlement patterns are volatile and/or spatially synchronised. Finally, we observe recovery of depleted populations, following fishery closures, can vary by over a decade depending on post-closure dispersal patterns. These findings expose how dispersal variability creates substantial, previously unrecognized risks for marine population management.