Septic tank irrigation systems are widely used for decentralized wastewater management. While effective in treatment, their environmental impacts, particularly on soil microbial processes and resulting greenhouse gas (GHG) emissions are not well understood. This study examined soil microbial contributions to GHG fluxes from irrigated and non-irrigated plots using soil flux measurements in the field and microbial enzyme assays in the lab. Results showed negative fluxes of methane (CH₄) and nitrous oxide (N₂O) in control plots, indicating net uptake, while carbon dioxide (CO₂) exhibited positive fluxes. Statistically significant differences in CH₄ and N₂O fluxes were observed between irrigated and non-irrigated zones, with cumulative mean fluxes higher for all three GHG in irrigated soils. Soil and water quality assessments revealed elevated pH, hardness, and nutrient loads, particularly ammonium and orthophosphate, exceeding EPA-recommended thresholds. In-vitro targeted enzymatic assays for mcrA and nosZ indicated elevated potential for CH₄ and N₂O production in the treated zone. Amplicon sequencing of microbial communities showed distinct differences in taxonomic composition and functional gene diversity, including a heterogeneous distribution of mcrA in irrigated soils. Quantitative PCR revealed significantly higher abundance of nosZ operational taxonomic unit 1, which encodes nitrous oxide reductase, in the irrigated plot. Overall, the study highlights that septic tank irrigation systems can alter microbial activity and increase trace gas emissions, suggesting potential adverse effects on ecosystem function and the need for revised management strategies.