Recent increases in the magnitude and frequency of disturbances affecting coral reefs have caused declines in coral cover, which have caused shifts in their benthic community composition. Such changes are striking on coral reefs that have undergone bleaching or have been damaged by tropical storms, after which, phase shifts from coral to algal domination are common. Whether coral communities return to a similar percent cover of coral after disturbances is determined by the success of key ecological processes such as pre- and post-settlement events. Pre- and post- settlement processes influence the spatial distribution and abundance of adult corals, thus determining the ability of the reef to become resilient to disturbances, or to recover coral community structure and function. In these studies, I investigate how the interactions between environmental pressures and physical features of the seafloor (i.e., microhabitats (mm to cm)) influence coral recruitment in the South Pacific (Moorea, French Polynesia, and Caribbean (St. John, US Virgin). In Moorea, I quantified how microhabitats (i.e., crevices on hard benthic substrata) can be recreated through 3-dimensional printing to better understand how those spaces can promote the settlement and physiology (i.e., net calcification and dark-adapted quantum yield) of reef corals in disturbed reefs. In the Caribbean, I explored how algal communities, and its associated benthic grazers at small scales (mm to cm) affect the spatial distribution of corals. In Moorea, microhabitats promoted higher coral densities more than predicted by chance alone. On 3D printed tiles, a higher percentage of Pocillopora acuta settled within imprinted microhabitats relative to smooth tiles. In St. John, algal turf relative to other environmental factors explained 26% of the variation in the distribution of small corals across reef sites. Small corals within algal turf patches were found with more tissue necrosis around their edges than small corals outside algal turf patches. These results highlight the importance of fine scale features of coral reefs in mediating recruitment patterns, while underscoring the opportunities to enhance recruitment through 3D printing techniques with potential for wider restorative application.