The worlds’ coral reefs are in decline. Active reef restoration is increasingly seen as a viable method for reversing this decline in many locations. Coral will be grown in onshore aquaculture facilities and deployed to specified reef locations in the wild. The industry is still in its infancy, presenting significant opportunities to optimize this coral production. We formulate and solve the first mathematical programming model of this coral aquaculture facility location and sizing problem using a two-stage algorithm and standard linear mixed-integer solver. Our results inform strategic decisions regarding the number, location, and sizing of facilities, as well as operational decisions of growth time for coral in a facility to minimize total costs. Residence time in a facility is assessed in terms of its impact on coral survival, production demand, and facility throughput. Computational experiments demonstrate the sensitivity of optimal facility number and location to changes in the reefs restored and the relative weighting of cost parameters. The relationship between residence time and coral survival is shown to be critical to optimizing operational decisions. These results inform the value of data certainty to optimize the logistics of coral aquaculture production.