Using a comprehensive data set (dissolved CH(4), δ(13)C-CH(4), δ(2)H-CH(4), δ(13)C-DIC, δ(37)Cl, δ(2)H-H(2)O, δ(18)O-H(2)O, Na, K, Ca, Mg, HCO(3), Cl, Br, SO(4), NO(3) and DO), in combination with a novel application of isometric log ratios, this study describes hydrochemical and thermodynamic controls on dissolved CH(4) from a coal seam gas reservoir and an alluvial aquifer in the Condamine catchment, eastern Surat/north-western Clarence-Moreton basins, Australia. δ(13)C-CH(4) data in the gas reservoir (−58‰ to −49‰) and shallow coal measures underlying the alluvium (−80‰ to −65‰) are distinct. CO(2) reduction is the dominant methanogenic pathway in all aquifers, and it is controlled by SO(4) concentrations and competition for reactants such as H(2). At isolated, brackish sites in the shallow coal measures and alluvium, highly depleted δ(2)H-CH(4) (<310‰) indicate acetoclastic methanogenesis where SO(4) concentrations inhibit CO(2) reduction. Evidence of CH(4) migration from the deep gas reservoir (200–500 m) to the shallow coal measures (<200 m) or the alluvium was not observed. The study demonstrates the importance of understanding CH(4) at different depth profiles within and between aquifers. Further research, including culturing studies of microbial consortia, will improve our understanding of the occurrence of CH(4) within and between aquifers in these basins