Sea level rise increases the frequency and intensity of saltwater intrusion events, and it affects the soil biogeochemical cycle in estuarine freshwater and brackish wetlands. A laboratory study measured the methane production potentials during from the topsoil of two freshwater Cyperus malaccensis marshes and two brackish C. malaccensis marshes during 12 days of incubation when exposed to varying salinities (0, 5, 10, 15, and 21 g/L of seawater or salt [NaCl] solutions). Seawater addition with a salinity range from 5 to 21 g/L induced a progressive suppression of methane production potentials. For all levels of salinity, except the freshwater control, more than 93% of methane production potential was inhibited, whereas there was no significant difference of suppression effects on methane production potentials upon the addition of seawater with a salinity range from 10 to 21 g/L. Ionic stress (represented by NaCl) reduced methane production potentials in both 15 and 21 g/L NaCl addition treatments; 5 and 10 g/L NaCl treatments did not significantly reduce methane production potentials (percentage of inhibition was less than 30%). Our results indicate that SO₄^2- reduction, not osmotic stress by chloride ions, is the main process suppressing methane production in estuarine freshwater and brackish marshes following seawater intrusion.