Onsite wastewater treatment systems service more than 1 in 5 households in the U.S. In spite of their prevalence, the subsurface soil-dispersal component of these systems (e.g. septic tank leach fields) is understudied in terms of its air and water quality impacts. Treatment performance of these systems is seldom monitored, particularly with regards to greenhouse gas (GHG) emissions such as methane (CH4), nitrous oxide (N2O), and carbon dioxide (CO2). Additionally, microbial controls on GHG cycling in these soil-based treatment systems are poorly understood. This work aimed to elucidate the link between atmospheric GHG emissions from leach field and control lawns, and distribution and activity of microbial populations directly involved in GHG cycling. In particular, we examined the effect of soil volumetric water content (VWC), both by sustained flooding and a precipitation event, on surface GHG fluxes, subsurface production, and distribution and activity of GHG cycling microbial populations in leach field and control lawns. Functional genes for production and consumption of CH4 (mcrA and pmoA, respectively) and N2O (cnorB and nosZ, respectively) were used to quantify in situ presence and activity of these key GHG cycling populations. In the first study, leach field and control lawn GHG emissions, soil VWC, and microbial community presence and distribution (with a focus on CH4 cycling populations) were measured at nine sites in central New York. Results from this study suggested microbial communities did not differ between control and leach field lawns except under flooded conditions. High soil VWC drove CH4 emissions and gene abundances of mcrA and pmoA but was not a significant driver of N2O fluxes or biomarker genes. In the second study we aimed to explore the relationship between flooding and GHG cycling in leach field soils. Leach field soil columns were constructed in lab to monitor performance of these systems under either well-maintained or failing-by-flooding conditions. The columns were compared in their surface CH4 flux, subsurface CH4 production, distribution, presence, and activity of microbial communities involved in CH4 cycling, and nutrient (nitrogen and phosphorus) and chemical oxygen demand (COD) removal. Results indicated flooding significantly increases CH4 production in leach field soils and decreases both COD removal and diversity of soil microbial communities. The final study examined the effect of rainfall on GHG fluxes and subsurface profiles in soils above an active leach field system. GHG measurements were coupled to quantification of biomarker abundances for CH4 and N2O cycling populations. This study revealed that all GHG fluxes increase after a rain event but trends vary by compound. Additionally, transcript abundances were not reliable indicators of increases in atmospheric GHG fluxes after a rain event.