Soil CO₂ efflux represents a crucial component of mangrove carbon cycling, yet its spatial and seasonal variability remains poorly constrained in Amazonian coastal systems. An evaluation of CO₂ emissions was conducted across three contrasting mangrove physiognomies on the Ajuruteua Peninsula to investigate how edaphic characteristics, hydrological conditions, and salinity regimes shape soil–atmosphere exchanges. Distinct patterns emerged among sites, reflecting differences in soil texture, water saturation, organic matter content, and salinity dynamics driven by rainfall seasonality and tidal influence. CO₂ emissions were consistently higher in less saline areas and were strongly constrained in highly saline scrub formations, underscoring the inhibitory effect of salt accumulation on microbial activity and gas transport. Principal component and regression analyses highlighted complex interactions between soil properties and environmental drivers. Findings demonstrate how mangrove structural heterogeneity, hydrology, and salinity gradients regulate CO₂ efflux and underscore the need to incorporate physiognomic complexity into carbon-budget assessments across tropical coastal wetlands.