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[Display omitted] • Wastewater significantly stimulated GHG productions in the mangrove and salt marsh sediments. • Salt marshes had much higher CO 2 and CH 4 emissions and lower N 2 O emissions than mangroves with wastewater input. • The saltmarsh sediments with wastewater input had less global warming potential than mangrove sediments. Wastewater discharge and salt marsh invasion are two main disturbances in global mangrove wetland ecosystems, but their combined effects on greenhouse gas (GHG) emissions remain unclear. Here, we performed a laboratory incubation experiment by adding wastewater (aquaculture and domestic wastewater) to mangrove and salt marsh sediments. Dissolved GHGs (CO 2 , CH 4 and N 2 O) and environmental parameters were measured over a time series of 50 days. The nitrification and denitrification rates and corresponding functional gene abundances (AOA, AOB, nirS , and narG) were also quantified. The results show that wastewater addition significantly increased GHG emissions and global warming potential (GWP) in wetland sediments (p < 0.05 for both). Compared with mangroves, salt marsh sediments produced more carbon GHGs (CO 2 and CH 4) but less N 2 O after wastewater input. These different stimulatory effects could be explained by the nitrogen and carbon substrate availability, organic matter quality, and functional gene abundances in sediments. Assessing GHG emissions as CO 2 equivalents, future scenarios of increasing salt marsh invasion with wastewater addition would increase the GWP caused by CO 2 and CH 4 , decrease blue carbon sequestration potential in wetlands, and decrease the GWP caused by N 2 O and total GWP, indicating a great impact on global climate change and important implications for managing coastal wetlands. [ABSTRACT FROM AUTHOR]