Coastal wetlands capture carbon dioxide from the atmosphere at high rates and store large amounts of “blue carbon” in soils. These habitats are home to a variety of microbial communities that break down organic matter and cycle nutrients, playing a substantial role in coastal biogeochemical balance. Rising sea levels make coastal wetlands more susceptible to saltwater intrusion, which might disrupt biogeochemical processes, such as the sulfur cycle and methane generation/consumption by bacteria thus disrupting existing equilibria. A change in biogeochemical equilibria may produce important climate-related feedback because these systems, while involved in carbon sequestration, also have the potential to emit greenhouse gases, with reported higher emissions in freshwater ecosystems compared to brackish ones. In this study, we characterize the microbial community and geochemical properties in soils of three temperate coastal wetlands along a salinity gradient to assess the effect of salinity on organic matter decomposition and related greenhouse gas emissions. The full-length Oxford Nanopore MinION 16S rRNA amplicon sequencing is used to characterize bacterial communities from soil samples. Results indicate a prevalence of sulfur-reducing bacteria in salinized sites compared to freshwater sites. In brackish environments, there is an emergence of obligate anaerobic taxa associated with sulfate reduction, fatty acid degradation, and denitrifying bacteria. These microbial communities play a significant role in reducing CH4 emissions while simultaneously increasing CO2 emissions within these habitats. This study reveals the structure of microbial communities in wetland soils, crucial for ecosystem understanding and implications in wetland conservation, management, and climate change mitigation.