Anthropogenic impacts and climate change are increasing the frequency and intensity at which ecosystems are being perturbed. On tropical reefs, disturbances can result in loss of live coral and sometimes initiate a transition to an alternative community state, frequently one dominated by macroalgae. Because algae-dominated reefs may have lower productivity, decreased species diversity and reduced ecosystem services, there has been considerable interest in elucidating the mechanisms that mediate a transition to an algae dominated state or the re-establishment of coral. In this dissertation I explore how physical attributes of a coral reef and the echinoid and fish communities control algal growth and influence the return to coral dominance. Recent disturbances in Moorea, French Polynesia offer an opportunity to examine the effects of architectural complexity of the substrate on recruitment of new coral colonists. I explore how the success of new coral colonists is affected by variation in structural complexity, particularly with respect to the skeletons of recently-killed branching coral. I quantified growth and survival of juvenile pocilloporid corals on structurally complex Pocillopora skeletons and on massive Porites, then generated quantitative predictions about the role these different types of substrates play in the replenishment of coral populations in the lagoons of Moorea. Results revealed that recruitment to dead branching Pocillopora structures is high, yet very low subsequent survival of those recruits, due to fast erosion of their host, indicates that dead Pocillopora structures are a sink for corals at vulnerable life stages. Microhabitats on dead coral structure can also provide important habitat for new coral colonists. Survivorship of young corals can be greater in crevices and holes than on exposed surfaces, due to incidental or targeted predation by herbivores and corallivores. Thus, other taxa that influence the availability of crevice space can indirectly mediate coral recruitment. Bioeroding echinoids have the potential to affect settlement and early survival of corals through their influence on crustose coralline algae (CCA) and/or the provision of crevice space. In Moorea, the echinoid Echinometra mathaei create distinctive crevices that enhance the small-scale structural complexity of the reef and are associated with high cover of CCA within and surrounding them. This study demonstrates that the microhabitats created by E. mathaei on slower eroding Porites coral provide favorable habitat for recruitment of coral, thereby bioeroding sea urchins could have an overall positive impact on the coral community. In 2013, an unknown agent resulted in rapid mortality of echinoid populations in the lagoon of Moorea. In the final portion of this dissertation, I describe the nature of the decline in D. savignyi populations, and report how the benthic community responded over the first 2.5 years following the abrupt mortality event. Additionally, I experimentally tested the ability for fish and remaining sea urchin herbivores to control algal growth on this reef and determined the rate of algal colonization in the absence of these herbivores. Despite high abundances prior to their demise, the loss of D. savignyi did not result in an increase in macroalgae or a shift in community structure. The experimental results suggest that fish herbivores were able to compensate for the loss of the echinoids by rapidly consuming any enhanced algal growth. Furthermore, the establishment of algae in Moorea appears more slow than may occur on other tropical reefs in the absence of herbivory.