Abstract In view of current worldwide coral reef decline, and the shortcomings of traditional top‐down management schemes of Marine Protected Areas (MPAs), decision makers and scientists face the important challenge of developing new approaches to generate effective conservation strategies. This study evaluates MPAs as linked social–ecological systems (SES) to inform better management by calculating indices for ecological health, social adaptive capacity, and the impact intensity of overfishing, pollution, and tourism. A series of ecological and socioeconomic indicators are used to estimate these indices and determine relevant conservation strategies in two protected areas in the Colombian Caribbean. Results reveal a precarious situation of high impact intensity combined with low ecological health and adaptive capacity. This study provides further evidence supporting the need for reconciliation of SES and a framework by which decision makers can assess priorities to increase MPA effectiveness. We highlight the need for system reorganization and recommend bottom‐up comanagement schemes as a priority strategy to strengthen adaptive capacity.