AbstractMass mortality of the sea urchin Diadema antillarum due to disease outbreaks in 1983 and 1991 decimated populations in the Florida Keys, and they have yet to recover. Here, we use a coupled advection–diffusion and fertilization–kinetics model to test the hypothesis that these populations are fertilization limited. We found that fertilization success was ≥ 96% prior to the first disease outbreak, decreased substantially following recurrent disease to 3%, and has since remained low. By investigating the combined effects of physical factors (population spatial extent and current velocity) and sea urchin behavior (aggregation) on density‐dependent fertilization success, we show that fertilization success at a given density increases with increasing population spatial extent and decreasing current velocity, and is greater under simulated aggregation behavior of D. antillarum. However, at present population densities, the increase in fertilization success due to aggregation is < 1%, even under the most favorable physical conditions. These results indicate that populations are severely fertilization limited, and that Allee effects at low population density will continue to limit recovery. Our results can serve as a practical guide to managers in the development of coral reef restoration strategies, including the design of a D. antillarum restocking program to obtain reproductively viable populations.