Shale - water - CO2 reactions may occur during CO2 geological storage, enhanced gas recovery, enhanced oil recovery, or supercritical CO2 fracturing. Shale-acid reactions occur during fracturing or acid stimulation. The mobilisation of metals from these processes can be an environmental concern if production water leaks or is released at surface. In addition, reactions may cause changes at the pore scale and affect gas or fluid flow. Three gas shales from the Australian Cooper Basin REM sequence were characterised for metals in minerals by synchrotron X-ray fluorescence microscopy. Metals including Zn, As, Ni, Cr were hosted in sphalerite associated with organic matter, Pb was in pyrite cement, and Mn was hosted in siderite. The shales were separately reacted with brine and supercritical CO2, with CO2-SO2, with dilute HCl, or with N2 at 100 °C and 20 MPa in batch reactors. The solution pH decreased during mineral reactions releasing metals to solution with the general concentrations from reaction with HCl > CO2-SO2 > CO2 > N2 and brine. Of the total available Pb, As, Li, and Zn in the shales, from 0 to 17%, 0.3 to 23%, 3 to 13%, and 0.4 to 28% was released to solution respectively. Corrosion of siderite and ankerite was observed after the CO2 reactions, with precipitation of Fe-oxides. After CO2-SO2 reaction siderite and ankerite were dissolved with pyrite, barite, and Fe-rich precipitates. HCl reactions resulted in complete dissolution of carbonates, with dissolution pits and no mineral precipitation observed. The changes to the fractions of gas accessible mesopores were characterised by small angle neutron scattering (SANS). The Epsilon Formation had the greatest fraction of open accessible pores in the SANS range of 10 to 150 nm, followed by the Murteree and Roseneath shale samples. After CO2 or CO2-SO2 reactions a small decrease in pore accessibility was more pronounced in the Murteree and Roseneath shales, consistent with mineral precipitation. HCl reaction resulted in opening of pores at 150 nm and closing of the smallest measured pores at 10 nm. Metals were mobilised from siderite, ankerite and sulphide minerals mainly, and were dependent on the mineral and metal content but also on the injected gas stream or fluid composition. CO2 based fluids may result in cleaner flow back water, than HCl based fluids. Geochemical reactions during CO2 storage or acid treatment in reactive shales cause pore changes that can affect gas migration. Mineral precipitation during CO2 and CO2-SO2 reactions can result in favourable self-sealing.