Coastal intertidal wetlands are dynamic and biodiverse habitats with carbon-rich waterlogged soils. When the soil gets exposed to oxygen, carbon can be emitted as CO2 back into the atmosphere. In this study we investigate whether contrasting stepped vs. gradual marsh edge topography, resulting from lateral cliff erosion versus expansion influences the soil-atmosphere CO2 fluxes. CO2 fluxes were quantified alongside groundwater level, soil temperature, and local sediment grain size across an estuarine salt marsh with differing seaward edge topography. We found that the CO2 flux from the marsh soil was on average greater at cliffed-eroding compared to sloped-prograding sites, 1.11 ± 0.77 g/m2 hr−1 and 0.88 ± 0.74 g/m2 hr−1, respectively. The presented CO2 emissions from the soil to the atmosphere consider the static morphology, i.e., the fluxes from the soil as it sits in place during the respective measurement. Soil respiration varied temporally with tidal cycle, groundwater levels, soil temperature, and spatially with distance to the seaward vegetation edge. Overall, fluxes during a neap cycle were significantly larger compared to spring tidal cycles. Our study thus highlights that soil CO2 efflux is affected by marsh topography resulting from cliff formation and marsh edge undercutting. The eroding and prograding sites differed in their site characteristics related to groundwater level, grain size and soil temperature, influencing the soil to atmosphere CO2 flux from the remaining marsh platform. Our findings highlight the spatial and temporal variability of carbon fluxes in a salt marsh environment and the importance of geomorphic form and process in understanding coastal carbon dynamics.