Emissions of methane (CH4), a major greenhouse gas, should be cut by at least 30% by 2030 according to the last Conference of the Parties, CoP26. Aquaculture pond is a major CH4 emitter, yet the microbial mechanisms ruling methanogenesis by degradation of organic matter in sediments remain unclear. In particular, the respective roles of hydrogenotrophic and acetoclastic methanogenesis, and the impact of aquaculture farming practices are unknown. We studied methanogenesis in the surface sediments from a freshwater and an oligohaline pond before, during, and after shrimp farming. Hydrogenotrophic and acetoclastic contributions were distinguished by acetoclastic inhibition with methylfluoride (CH 3 F), and by 13 C-analysis of CO 2 and CH 4. We also monitored the methanogenic community structure, dissolved organic carbon (DOC) levels, carbon to nitrogen (C/N) ratios, and humification indices derived from Fourier transform infrared spectroscopy. The results reveal that aquaculture farming practices increased methanogenesis rates, and these increases were explained by higher levels of DOC and lower C/N ratios during farming. Of the total methane produced, 51%-78% was by hydrogenotrophic methanogenesis. However, the total methane contribution from acetoclastic methanogenesis increased from approximately 22% before farming to approximately 45% during and after farming, with a decreasing isotope fractionation factor αc and an increasing relative abundance of Methanosaeta acetoclastic methanogen. All humification indices decreased during and after farming compared to before farming due to the input of polysaccharide-rich aquafeed. The close relationship between the humification indices and methanogenesis pathways indicates that the changes in sediment substrate quality drove the variation in the methanogenesis pathways. Increases in salinity decreased the methanogenesis rates but did not change the methanogenesis pathways. Overall, our findings reveal that aquaculture farming practices increase methanogenesis rates and favor acetoclastic over hydrogenotrophic methanogenesis, and that adjusting shrimp diets, increasing salinity, and removing residual aquafeed could reduce methanogenesis.