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Abstract Coastal wetlands play a vital role in the global carbon cycle and are under pressure from multiple anthropogenic influences. Altered hydrology and land use change increase susceptibility of wetlands to sea‐level rise, saltwater intrusion, tidal flood events, and storm surges. Flooding from perigean spring tides and storm surges rapidly inundates coastal wetlands with saline waters, quickly surpassing vegetation tolerances, leading to shifts in soil microbial respiration, peat collapse, and plant mortality, followed by establishment of salt‐tolerant vegetation. The Southeast Saline Everglades (SESE) is facing many of these pressures, making it a model system to examine the impacts of ecosystem state transitions and their carbon dynamics. Saltwater flooding from Hurricane Irma (2017) initiated a transitional state, where less salt‐tolerant vegetation (e.g.,Cladium jamaicense) is declining, allowing halophytic species such asRhizophora mangleto colonize, altering the ecosystem's biogeochemistry. We utilized eddy covariance techniques in the SESE to measure ecosystem fluxes of CO₂and CH₄in an area that is transitioning to an alternative state. The landward expansion of mangroves is increasing leaf area, leading to greater physiological activity and higher biomass. Our site was presented initially as a small C source (47.0 g C m⁻²) in 2020, and by 2022 was a sink (−84.24 g C m⁻²), with annual greenhouse carbon balance ranging from −0.04 to 0.18. Net radiative forcing ranged from 2.04 to 2.27 W m⁻² d⁻¹. As the mangrove landward margin expands, this may lead the area to become a greater carbon sink and a potential offset to increasing atmospheric CO₂concentrations.