A common assumption in the geological analysis of modern reefs is that coral community zonation seen on the surface should also be found in cores from the reef interior. Such assumptions not only underestimate the impact of tropical storms on reef facies development, but have been difficult to test because of restrictions imposed by narrow-diameter cores and poor recovery. That assumption is tested here using large-diameter cores recovered from a range of common zones across three Campeche Bank reefs. It is found that cores from the reef-front, crest, flat and rubble-cay zones are similar in texture and coral composition, making it impossible to recognize coral assemblages that reflect the surface zonation. Taphonomic signatures imparted by variations in encrustation, bioerosion and cementation, however, produce distinct facies and delineate a clear depth zonation. Cores from the reef-front zone (2–10 m depth) are characterized by sections of Acropora palmata cobble gravel interspersed with sections of in-place (but truncated) A. palmata stumps. Upper surfaces of truncated colonies are intensely bioeroded by traces of Entobia isp. and Gastrochaenolites isp. and encrusted by mm-thick crustose corallines before colony regeneration and, therefore, indicate punctuated growth resulting from a hurricane-induced cycle of destruction and regeneration. Cores from the reef crest/flat (0–2 m depth) are also characterized by sections of hurricane-derived A. palmata cobble-gravels as well as in-place A. palmata colonies. In contrast to the reef front, however, these cobble gravels are encrusted by cm-thick crusts of intergrown coralline algae, low-relief Homotrema and vermetids, bored by traces of Entobia isp. and Trypanites isp. and coated by a dense, peloidal, micrite cement. Cores from the inter- to supratidal rubble-cay zone (+0–5 m) are only composed of A. palmata cobble gravels and, although clasts show evidence of subtidal encrustation and bioerosion, these always represent processes that occurred before deposition on the cay. Instead, these gravels are distinguished on the basis of their limited bioerosion and marine cements, which exhibit fabrics formed in the intertidal zone. These results confirm that hurricanes have a major influence on facies development in Campeche Bank reefs. Instead of reflecting the surface coral zonation, each facies records a distinctive, depth-related set of taphonomic processes, which reflect colonization, alteration and stabilization following the production of new substrates by hurricanes.