Growth rates of the major Caribbean reef framework building coral Orbicella spp. decrease with increasing water depth and light attenuation. However, reliable, spatially distributed growth rates for corals deeper than 30 m are rare, and the combined influence of coral framework accretion, secondary framework accretion, and framework macroboring on net framework calcification in these habitats is poorly constrained. To better understand the growth limits and spatial variability of Orbicella-dominated mesophotic coral reef ecosystems, live platy samples of Orbicella franksi were collected at 3 south Puerto Rican Shelf upper mesophotic reef habitats with varying structural characteristics. Average mesophotic coral linear extension rates, determined by standard X-radiographic techniques and confirmed by stable isotopic analyses, were 0.80 mm/yr ± 0.03 SE, slower than previously recorded for Orbicella spp. at shallower U. S. Virgin Island reefs. However, coral cover at 2 of the mesophotic reefs was considerably higher than at nearby shallow-water reefs, implying that fast coral growth rates are not necessarily needed to maintain Caribbean reefs with high coral cover and structural complexity. A probable reason for this is reduced bioerosion with depth. Rates of net coral framework calcification were significantly different between the neighboring mesophotic coral reef habitats, likely a result of the complex interplay between site variability in irradiance, nutrient availability, and other factors. Analysis also indicated that the influence of El Niño–Southern Oscillation on water circulation and salinity as well as on water clarity and nutrient distribution in the Caribbean is reflected in the annual variability of mesophotic O. franksi growth rates. Site differences in net coral framework calcification suggest a potential long-term mechanism for the production or maintenance of heterogeneous reef-scale geomorphology along broad-sloping carbonate shelves colonized with mesophotic coral reef systems.