The persistence and resilience of marginal shallow coral reefs at their limits of environmental tolerance have declined due to chronic environmental degradation and climate change. However, the consequences for the natural recovery ability of reefs of disturbance remain poorly understood. This study considered the potential for natural recovery through coral recruitment on fringing reefs across different geographic regions under contrasting environmental conditions in Puerto Rico. Reefs in areas with significant water quality degradation and more severe physical impacts of hurricanes were expected to have lower coral recruit density and diversity, and therefore less potential for recovery. Sixteen reefs were assessed across three geographic regions. Degraded reefs sustained a lower percentage of live coral cover and had higher macroalgae and turf algae abundance. Locations affected by high PO4, NH3+ and optical brightness concentrations, high turbidity, and high sea surface temperature anomalies, chlorophyll-a concentration and light attenuation Kd490 evidenced significantly lower coral recruit density and diversity. Hurricane-decimated reefs also exhibited impoverished coral recruit assemblages. Low coral recruitment could have important long-term implications under projected climate change and sea level rise, particularly in coastal urban habitats. There is a need to implement effective environmental conservation, ecological restoration and community participation strategies that facilitate enhanced coral recruitment success and assisted recovery processes.