Carbon dioxide exchange between the atmosphere and forested subtropical wetlands is largely unknown. Here we report a first step in characterizing this atmospheric–ecosystem carbon (C) exchange, for cypress strands and pine forests in the Greater Everglades of Florida as measured with eddy covariance methods at three locations (Cypress Swamp, Dwarf Cypress and Pine Upland) for 2 years. Links between water and C cycles are also examined at these three sites, as are methane emission measured only at the Dwarf Cypress site. Each forested wetland showed net C uptake from the atmosphere both monthly and annually, as indicated by the net ecosystem exchange (NEE) of carbon dioxide (CO₂). For this study, NEE is the difference between photosynthesis and respiration, with negative values representing uptake from the atmosphere that is retained in the ecosystem or transported laterally via overland flow (unmeasured for this study). Atmospheric C uptake (NEE) was greatest at the Cypress Swampp (−900 to −1000 g C m² yr⁻¹), moderate at the Pine Upland (−650 to −700 g C m² yr⁻¹) and least at the Dwarf Cypress (−400 to −450 g C m² yr⁻¹). Changes in NEE were clearly a function of seasonality in solar insolation, air temperature and flooding, which suppressed heterotrophic soil respiration. We also note that changes in the satellite-derived enhanced vegetation index (EVI) served as a useful surrogate for changes in NEE at these forested wetland sites.