Community structure, environmental conditions, and lesion regeneration in a reef-building coral species was assessed to compare the resilience of patch reefs in two areas of varying human impact in the Exuma Cays of the Bahamas. The Exuma Cays Land and Sea Park (ECLSP) is a well-established no-take marine protected area which is minimally influenced by human activities. Elizabeth Harbour (EH) and the adjacent Moriah Harbour Cay National Park are both threatened by multiple sources of pollution, habitat destruction, and fishing. Indicators of resilience were measured at the community, population, and organismal (individual) level in order to identify potential relationships between environmental factors, reef condition, and lesion regeneration capacity of an important reef-building coral species, Montastraea faveolata. Benthic surveys revealed that in contrast to patch reefs in the ECLSP, the reefs of EH are now algal dominated systems. Reefs in the ECLSP were less impacted by algal growth as macroalgal cover was extremely low at 3 of 4 study sites (<10%). A highly significant difference was found in algal mat cover between the two areas. Mean lesion regeneration rates were consistently greater in the ECLSP, though a significant difference was found only during the first sampling period. Variation was greater within reefs and within colonies than between reefs and between colonies. Analysis of these results indicates a significant negative correlation between intra-colony variation and regeneration after 5 days. This study provides additional ecological data which confirms the degraded condition of reefs in Elizabeth Harbour and explores lesion regeneration as a potential management tool in detecting reef resilience.