Using a comprehensive data set (dissolved CH₄, δ¹³C-CH₄, δ²H-CH₄, δ¹³C-DIC, δ³⁷Cl, δ²H-H₂O, δ¹⁸O-H₂O, Na, K, Ca, Mg, HCO₃, Cl, Br, SO₄, NO₃ and DO), in combination with a novel application of isometric log ratios, this study describes hydrochemical and thermodynamic controls on dissolved CH₄ from a coal seam gas reservoir and an alluvial aquifer in the Condamine catchment, eastern Surat/north-western Clarence-Moreton basins, Australia. δ¹³C-CH₄ data in the gas reservoir (−58‰ to −49‰) and shallow coal measures underlying the alluvium (−80‰ to −65‰) are distinct. CO₂ reduction is the dominant methanogenic pathway in all aquifers, and it is controlled by SO₄ concentrations and competition for reactants such as H₂. At isolated, brackish sites in the shallow coal measures and alluvium, highly depleted δ²H-CH₄ (<310‰) indicate acetoclastic methanogenesis where SO₄ concentrations inhibit CO₂ reduction. Evidence of CH₄ 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 CH₄ at different depth profiles within and between aquifers. Further research, including culturing studies of microbial consortia, will improve our understanding of the occurrence of CH₄ within and between aquifers in these basins.