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Abstract Sea level rise and more frequent and larger storms will increase saltwater flooding in coastal terrestrial ecosystems, altering soil‐atmosphere CO₂and CH₄exchange. Understanding these impacts is particularly relevant in high‐latitude coastal soils that hold large carbon stocks but where the interaction of salinity and moisture on greenhouse gas flux remains unexplored. Here, we quantified the effects of salinity and moisture on CO₂and CH₄fluxes from low‐Arctic coastal soils from three landscape positions (two Wetlands and Upland Tundra) distinguished by elevation, flooding frequency, soil characteristics, and vegetation. We used a full factorial laboratory incubation experiment of three soil moisture levels (40%, 70%, or 100% saturation) and four salinity levels (freshwater, 3, 6, or 12 ppt). Salinity and soil moisture were important controls on CO₂and CH₄emissions across all landscape positions. In saturated soil, CO₂emissions increased with salinity in the lower elevation landscape positions but not in the Upland Tundra soil. Saturated soil was necessary for large CH₄emissions. CH₄emissions were greatest with low salinity, or after 11 weeks of incubation when SO₄²⁻was exhausted allowing for methanogenesis as the dominant mechanism of anaerobic respiration. In partially saturated soil, greater salinity suppressed CO₂production in all soils. CH₄fluxes were overall quite low, but increased between 3 and 6 ppt in the Tundra. In the future, a small increase in floodwater salinity may increase CO₂production while suppressing CH₄production; however, where water is impounded, CH₄production could become large, particularly in the landscapes most likely to flood.