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Mangrove wetlands are important ecosystems, yet human development coupled with climate change threatens mangroves and their large carbon stores. This study seeks to understand the soil carbon dynamics in hydrologically altered mangrove swamps by studying aboveground biomass estimates and belowground soil carbon concentrations in mangrove swamps with high, medium, and low levels of disturbance in Cataño, Jobos Bay, and Vieques, Puerto Rico. All three sites were affected by hurricane María in 2017, one year prior to the study. As a result of being hit by the Saffir-Simpson category 4 hurricane, the low-disturbance site had almost no living mangroves left during sampling. There was no correlation between level of hydrologic alteration and carbon storage, rather different patterns emerged for each of the three sites. At the highly disturbed location, belowground carbon mass averaged 0.048 ± 0.001 g-C cm−3 which increased with increased aboveground biomass. At the moderately disturbed location, belowground carbon mass averaged 0.047 ± 0.003 g-C cm−3 and corresponded to distance from open water. At the low-disturbed location, organic carbon was consistent between all sites and inorganic carbon concentrations controlled total carbon mass which averaged 0.048 ± 0.002 g-C cm−3. These results suggest that mangroves are adaptive and resilient and have the potential to retain their carbon storage capacities despite hydrologic alterations, but mass carbon storage within mangrove forests can be spatially variable in hydrologically altered conditions.