An eddy covariance system within ancillary meteorological instruments has been operated at the Shark River Mangrove AmeriFlux Site (SRK) in southwestern Everglades National Park since 2004 to understand the magnitude of and controls on carbon dioxide and energy exchange across the forest-atmosphere interface. In August 2010, a carbon dioxide and water vapor sampling system was installed to measure mixing ratios of these trace gases at heights of 1 m, 7.5 m, 12 m, 18 m, 24 m, and 27 m with sampling of all 6 ports in a 10 minute interval. Data that was collected extensively in 2010 and 2011 show various exchanges of carbon dioxide in the mid-dry season (early March) to the early start of the wet season (late May/early June). A profile analysis showed carbon dioxide concentrations at ~420 micro-mols in May near the surface level whereas early March mixing ratios were ~400 micro-mols CO₂ and August 2010 exhibited concentrations of about 375 micro-mols CO₂. The largest mixing ratio gradients occurred typically between 9AM – 10 AM in the morning with average differences of 26 micro-mols CO₂ between the 27 m and 1 m heights, and differences of 10 micro-mols CO₂ on average between 6PM – 7PM. As water stage increases, the carbon dioxide concentration gradient between 27 m and 1 m decreases. For instance, the maximum profile system estimate (4.5 mmol CO₂ m-2 s-1) was recorded when the water stage was -0.15 m, and the minimum profile system estimate (-5.65 mmol CO₂ m-2 s-1) was observed when the water stage was 0.31 m. Soil, leaf litter, pneumatophores, prop roots, and course woody debris release carbon dioxide from the surface, which is temporally stored near the ground at night but is eventually released into the atmosphere. However, these exchanges of carbon dioxide are suppressed during flood tides. When water levels inundate soil and mangrove roots, carbon dioxide mixing ratios near the surface (1 m and 7.5 m ports) are reduced at night, suggesting suppression of carbon dioxide exchange during flood tides. Comparing profile systems from different seasons and time of day also show strong variance in carbon dioxide concentration within the canopy, which are used to improve estimates of net ecosystem exchange of the greenhouse gas. Hourly carbon dioxide mixing ratios increase when the canopy boundary layer supports an unstable atmosphere and also when air temperature increased during the day. These variations also differ from season to season, as a significant difference of carbon dioxide concentration was observed from the wet to dry seasons. Understanding the relations between vertical profiles of carbon dioxide mixing rations and controls including the tide and seasonal changes in temperature and climates can explain the exchange of carbon dioxide in a natural preserve.