The ecology of tropical carbonate coasts, including coral reefs and rocky limestone shores, is susceptible to disturbance that may have linked effects on geomorphology. Biogeomorphology, which considers the interrelations between biological and geomorphological processes, is particularly well-suited toward the understanding of such carbonate systems. Field observations and experimentation on tropical and temperate coasts by both biologists and geomorphologists, and the development of ecological theory, have come to stress the importance not of stable, successional littoral communities but rather of nonequilibrial, multistate systems. These ideas now need to be incorporated into improved models of coastal dynamics. Case studies from the Central Pacific, the Caribbean and the western Indian Ocean illustrate the interactions between external environmental variability and internal biological processes. These studies show how changing the balance between bioconstructional and bioerosional processes can interrupt a system’s development and, in some cases, shift carbonate-based systems between healthy and degradational states. A better understanding of the spatial and temporal complexities present in carbonate coastal and shallow marine environments is an important precursor to effective coastal zone management on these prevalent tropical shorelines