Rivers and their adjacent riparian forests are intimately linked by the exchange of water, nutrients, and organic matter. Both riparian cottonwood trees and adjacent river sediments host microbial communities including archeal methanogens, supporting methane production and emission to the atmosphere. Here we combine microbial community and in vitro stable isotope analyses to characterize the drivers of methane cycling in distinct anoxic habitats (river sediments vs. riparian cottonwood stems) associated with the Oldman River, southern Alberta (Canada). We demonstrate that, differences in the chemical characteristics of organic matter support divergent microbial communities that generate methane from distinct metabolic pathways. Organic matter in river sediments had C/N ratios approximately 50‐fold lower than in tree stems and had more diverse dissolved organic components. Contrasting substrate availability between river sediment and tree stems was likely the primary mechanism for the greater microbial diversity in river sediments than in tree stems, the significantly different bacterial communities, and the trend toward differing abundance of methanogen orders. The methane carbon isotope composition (δ13C values) differed for the tree stem (−103.6‰ to −70.6‰) and river sediment (−55.1‰ to −48.4‰) environments, suggesting that methane was primarily produced via CO2‐reduction in tree stems by Methanobacteriales, while river sediments produced more methane through acetate fermentation primarily by Methanosarcinales. This study demonstrates the importance of organic matter quality and microbial community composition in driving metabolic processes contributing to methane production and emission in rivers and adjacent riparian forests.