Sea-level rise and saline water intrusion have caused a shortage of fresh water and affected agricultural areas globally. Besides inundation, the salinity could alter soil nitrogen and carbon cycling in coastal soils. To examine the effect of salinity, an incubation experiment was used to investigate soil nitrogen and carbon cycling from an acid sulfate soil and an alluvial soil with and without additional nitrogen and carbon sources. Four levels of saline solution of 0.03, 10, 16 and 21 dS m^–1 were used to submerge acid sulfate and alluvial soil samples in a 125-mL jar. The experimental jars were incubated in the dark at 25°C. Gas samples were collected over 4 weeks and analysed for nitrous oxide (N₂O), carbon dioxide (CO₂) and methane (CH₄). The results showed that salinity significantly decreased N₂O emissions from the acid sulfate soil but did not affect emissions from the alluvial soil. Addition of glucose and nitrate enhanced N₂O production in both salt-affected soils. Emissions of CO₂ were not different among the salinity treatments, whereas available carbon and nitrate promoted soil respiration. Changes in CH₄ fluxes over the 4-week incubation were the same for both soils, and substrate addition did not affect emissions in either soil. The findings indicate that salinity has altered carbon and nitrogen cycles in the acid sulfate soil, and future fertiliser and crop management will need to account for the changed nutrient cycling caused by saline water intrusion and climate change.