Studies integrating mangrove in-situ observations and remote sensing analysis for specific sites often lack precise estimates of carbon stocks over time frames that include disturbance events. This study quantifies change in mangrove area from 1985 to 2018 with Landsat time series analysis, estimates above and belowground stored carbon using field data, and evaluates aboveground carbon stock changes after the 2004 Category 4, Hurricane Charley, in J.N. “Ding” Darling National Wildlife Refuge. Two allometric equation methods yielding similar results were used to estimate aboveground carbon content in three mangrove species found in the refuge. Aboveground carbon contained 67 (SE = 2) MgC ha⁻¹ with a total refuge estimate of 74,504 MgC in 2018. Sediment contained 259 (SE = 28) MgC ha⁻¹ for a total of 288,008 MgC in the refuge. The initial reduction in mangrove area caused by Hurricane Charley was between 0.6% and 5.3%, equivalent to between 427 MgC and 3,599 MgC under three different scenarios of carbon loss. As a result of the hurricane, approximately 61 ha of mangroves were disturbed, of which 24 ha had recovered by 2018, with 37 ha (~3% of the pre-hurricane mangrove area) still not recovered 14 years after the event. The 37 ha of mangroves that have not recovered are located in a tidally restricted area of the refuge. A longer recovery time in this area will likely result in a greater loss of carbon storage than in the rest of the refuge.