Wetlands are important locations for the release of greenhouse gases, including carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). However, the specific mechanisms driving these emissions, particularly in semiarid wetland ecosystems, remain unclear. This study examined the spatial variability of greenhouse gas fluxes across different hydrological gradients and explored the influence of soil physicochemical and microbiological properties on these emissions within the Ulansuhai Wetland in northern China. A laboratory incubation experiment was conducted using soil samples collected in-situ from different hydrological zones. The relationships between greenhouse gas fluxes and soil properties, microbial communities, and functional genes were analyzed primarily using correlation analysis and structural equation modeling. The results demonstrated that the infra-littoral and supralittoral zones primarily contributed to CH4 and CO2 emissions, whereas the epilittoral zone was the primary source of N2O emissions and CH4 sinks. Variations in CH4, CO2, and N2O emission rates were driven by a combination of soil physicochemical properties (e.g., moisture content, total organic carbon, and nitrate concentrations) and dominant microbial abundances (e.g., Alphaproteobacteria and Thiobacillus). Additionally, the pmoA and nosZ genes encoding enzymes involved in CH4 and N2O production did not fully elucidate gas fluxes, highlighting the need to consider additional functional genes in greenhouse gas assessments. Our findings indicate the significance of soil environments and functional microorganisms in regulating carbon and nitrogen cycling processes. This knowledge can contribute to the development of strategies aimed at mitigating the greenhouse effect in semi-arid wetlands.