Replenishment of benthic marine populations typically involves “settlement” from pelagic larval to benthic juvenile habitats. Mortality during this transition has been unknown because of the difficulty of measuring propagule supply in open water. For three weeks, we compared the nocturnal passage of presettlement fishes across the barrier reef encircling Moorea Island (French Polynesia) with the abundance of benthic recruits in the back-reef lagoon on the following morning. During this time, >40,000 presettlement unicornfish, Naso unicornis entered our study area of ∼1 km2 with half arriving on just two nights. Using coupled Beverton-Holt functions to describe the decay of each cohort, we were able to predict the daily abundance of recruits and their final age structure from the presettlement inputs. The best model estimated that ∼61% of the potential settlers were lost between their nocturnal arrival and the following morning, independent of cohort size. Postsettlement mortality was density dependent, varying between 9% and 20% per day. We attribute all mortality to predation and suggest that high risk associated with settlement has shaped colonization strategies. Because fishing targets the survivors of this population bottleneck, aquarium fisheries may be more sustainable when sourced from pelagic juveniles.