Mechanisms and factors controlling greenhouse gases production in agricultural drains and ponds

• Ponds emitted up to 35 × more CH 4 and 8 × more N 2 O than drains. • Irrigation promoted hydrogenotrophic methanogenesis and N 2 O reduction. • Rainfall induced partial CH 4 oxidation in transient oxic microzones. • Isotopes confirmed heterotrophic denitrification as main N 2 O pathway. • A few high-emitting ponds contributed ∼78% of total GHG emissions. Agricultural drains and ponds are underexplored but potentially significant sources of greenhouse gases (GHGs). Yet, the microbial pathways responsible for CH 4 , CO 2 , and N 2 O production, and their responses to hydrological events, remain poorly understood. Here, we applied a multi-isotope framework (δ 13 C-CH 4 , δ 13 C-CO 2 , δ 15 N-N 2 O, δ 18 O-N 2 O, and N 2 O site preference) to quantify GHG production processes in agricultural drains and ponds in south-eastern Australia during rainfall and irrigation events. GHG concentrations and fluxes were consistently higher in ponds than in drains, with CH 4 contributing most emissions. δ 13 C-CH 4 values suggested the predominance of hydrogenotrophic methanogenesis under irrigation. In contrast, during rainfall events, higher δ 13 C-CH 4 values suggested partial CH 4 oxidation under transiently oxygenated conditions with a possible increase in acetoclastic methanogenesis. The 15 N SP values of N 2 O showed that heterotrophic denitrification dominated production, with evidence of partial N 2 O reduction in ponds. CO 2 concentrations were elevated but comparatively more variable and linked to hydrological events. Together, these findings reveal that agricultural ponds are hotspots of GHG emissions and act as dynamic biogeochemical reactors where nutrient inputs, redox conditions, and hydrological events jointly regulate GHG cycling. From a management perspective, small, high-emitting ponds and drains contribute disproportionately to farm-scale emissions, highlighting the urgent need to incorporate these water bodies into national GHG inventories.