Intensive carbonate and clay mineral authigenesis took place throughout the Late Permian Bowen–Gunnedah–Sydney basin system in eastern Australia. We conducted isotopic and trace element analyses of carbonate and clay minerals from clastic sedimentary rocks of the Gunnedah Basin and the Denison Trough in the Bowen Basin. Rb–Sr isochron age data of the illitic clays are consistent with episodic hydrothermal fluid flow events that occurred in association with Gondwana rifting accompanied by alkaline magmatism at ∼85 Ma and ∼95 Ma. Stable isotope data of carbonate and clay minerals from the Gunnedah Basin are indicative of meteoric waters from a high-latitude environment as the main fluid source, whereas trace element, Sr and Nd isotope data highlight mixing of meteoric fluids with magmatic and/or crustal components, with a possible input from marine carbonates for some samples. Trace metals, oxygen and strontium isotopes of dawsonites from the Denison Trough are interpreted to have been mobilised by fluids that interacted with evolved clastic sedimentary and marine carbonate end members. According to the carbon isotope data, CO2 for calcite and ankerite precipitation was sourced mainly from thermal degradation of organic matter and magmatism, whereas the CO2 used for dawsonite formation is inferred to have been derived from magmatic and marine sources. In the low permeability environments (particularly in coal seams), the increasing accumulation and oversaturation of CO2 particularly promote the precipitation of dawsonite.