Coastal saline soils are increasingly reclaimed for agricultural purposes through organic amendments and nutrient supplementation, yet their impacts on soil organic carbon (SOC) and inorganic carbon (SIC) dynamics remain poorly understood. A microcosmic incubation experiment with 13C-labeled corn stover and/or nitrogen (N) and phosphorus (P) additions was established to examine the contributions of SOC and SIC to soil total CO2 efflux and the associated microbial mechanisms. Corn stover addition increased soil NO3−-N, inorganic N, available P and potassium (K), and dissolved organic C (DOC) by 50 %, 41 %, 22 %, 8 % and 52 %, respectively, while nutrients alone increased them by 73 %, 170 %, 128 %, 10 % and 16 %. Total CO2 efflux rose by 35 % with stover and by 24 % with nutrients alone, but their combined application synergistically enhanced emissions by 87 %. Stover addition initially increased CO2 effluxes from both SIC and SOC when nutrients were not amended but reduced these fluxes when nutrients were supplied during the first week. Microbial diversity declined under both amendments, with a shift toward copiotrophic taxa (e.g. Salinimicrobium and Microbulbifer as keystone bacterial genera) and reduced resilience to disturbance. Notably, SIC contributed 25 %–40 % of total CO2 efflux, highlighting its sensitivity to agricultural management. These findings underscore that SIC dissolution-driven by microbial or chemical processes—plays a substantial role in coastal soil carbon emissions. Future research must clarify the mechanisms of carbonate dissolution to refine global C cycling models in the context of agricultural expansion into coastal mudflats.