Tropical mangrove forests are important carbon sinks, the soil being the main carbon reservoir. Understanding the variability and the key factors that control fluxes is critical to accounting for greenhouse gas (GHG) emissions, particularly in the current scenario of global climate change. This study is the first to quantify carbon dioxide (CO2) and methane (CH4) emissions using a dynamic chamber in natural mangrove soil of the Amazon. The plots for the trace gases study were allocated at contrasting topographic heights. The results showed that the mangrove soil of the Amazon estuary is a source of CO2 (6.66 g CO2 m−2 d−1) and CH4 (0.13 g CH4 m−2 d−1) to the atmosphere. The CO2 flux was higher in the high topography (7.86 g CO2 m−2 d−1) than in the low topography (4.73 g CO2 m−2 d−1) in the rainy season, and CH4 was higher in the low topography (0.13 g CH4 m−2 d−1) than in the high topography (0.01 g CH4 m−2 d−1) in the dry season. However, in the dry period, the low topography soil produced more CH4. Soil organic matter, carbon and nitrogen ratio (C/N), and redox potential influenced the annual and seasonal variation of CO2 emissions; however, they did not affect CH4 fluxes. The mangrove soil of the Amazon estuary produced 35.40 Mg CO2 eq. ha−1 yr−1. A total of 2.16 kg CO2 m−2 yr−1 needs to be sequestered by the mangrove ecosystem to counterbalance CH4 emissions.