Due to the natural content and structure of the groundwater, its treatment has been considered as one of the greenhouse gas (GHG) emissions resources. Many groundwater resources contain large amounts of methane (CH4) that result from geological reactions of the aquifers. Also, CH4 could occur due to the anaerobic biological conditions of resources in aquifers. Biochar that is a carbon-rich end-product of the pyrolysis process of various biomass wastes could be used as a GHG reduction technique. From this perspective, this study aimed to mitigate the CH4 emissions from groundwater treatment using biochar adsorption in Southeastern Turkey. This study is novel in that biochar adsorption has been carried out for the reduction of CH4 emissions from groundwater treatment. The other originality of this work is that biochar has been derived from malt dust that is an industrial and agricultural waste of the brewery industry, using slow pyrolysis. Groundwater samples were ensured from three observation wells located at Harran Plain in spring and autumn, and CH4 concentrations were measured using gas chromatography (GC). CH4 emission has been estimated using a newly developed model that contains CH4 concentrations, Henry’s Law constant, and Global Warming Potential (GWP) based on the IPCC approach. The recommended model has been validated using sensitivity analysis. Also, a Monte Carlo simulation was carried out to determine which parameter affects the formation of CH4 emissions. CH4 monitoring has been fulfilled before and after groundwater treatment using biochar derived from malt dust. The reduction in CH4 emission has been figured out according to the monitoring results. The optimum operating parameters of slow pyrolysis for biochar production and biochar adsorption process have been defined using the Box--Behnken Design method. According to Monte Carlo simulation, Dissolved oxygen (DO) and oxidation–reduction potential (ORP) are the main parameters which have a positive effect on CH4 emissions mitigation. The results revealed that malt dust-derived biochar could adsorb CH4 emissions from groundwater treatment. Approximately 14.5% of reduction in CH4 emissions from groundwater treatment has been reported using biochar adsorption. This study has given a future perspective to reduce CH4 emissions from groundwater treatment using biochar adsorption process.