The rapidly increasing world energy demand requires the development of deep earth energy extraction methods such as unconventional oil and gas production, including coal bed methane recovery (CBM) and utilisation of hot pore fluid in deep geothermal reservoirs. However, all these deep earth energy production methods are associated with huge wastewater (brine) production. Disposal of this brine has become a major challenge in the energy industry, as direct disposal is highly undesirable due to its organic and inorganic pollutant content and its high salinity. Re-injection of brine into deep aquifers is therefore a feasible option to overcome this issue and the flowability through the sedimentary formation or its permeability plays a major role in this process. However, most of previous works mainly focus on the homogenous formations and therefore the brine permeability of deep heterogeneous sandstone aquifers is still not well understood. This study intends to obtain a comprehensive knowledge of this process by conducting a series of core flooding experiments for brine injection into two types of clay rich sandstone, WWS and WGS, obtained from Marburg formation, Queensland, Australia along different bedding orientations and under different reservoir conditions. A series of core flooding tests were conducted on 38mm diameter and 150mm long cylindrical core samples and the pressure developments along the samples were recorded over time for a range of confining pressures (10–25MPa), temperatures (30–60°C), and injection over-pressures (4–20MPa). According to the results, brine permeability in clay rich sandstone increases with increasing injection over-pressure and reduces with increasing depth and aquifer temperature. Furthermore, the flow characteristics of sandstone aquifers are largely dependent on their heterogeneous nature, and the presence of authigenic quartz, clay depositions, low permeable beddings and their orientation have significant influences on reservoir permeability. A stepped pattern was observed in the pore pressure development along the tested sandstone cores which depicts a possible pore structure variation during the fluid injection. A rapid pressure development occurs throughout the sample at the initial stage of injection may be due to the flux tends to pass through the preferable flow paths in the rock mass and then over the time this pressure development diminishes, possibly due to the gradual building of flow barriers by grain particles extracted from the initial rapid flux. These flow barriers obstruct the expected flow towards the downstream and cease the flow for some time until the pressure builds up steadily up to a certain level as it can break the flow barrier by re-arranging the pore structure. The existence of beddings further delays the demolishment of this barrier and beddings perpendicular to the flow direction creates a greater permeability reduction in the aquifer than parallel beddings, because the influence of these low permeable zones on permeability depends on the extent to which they limit the flowability across the rock mass. The experimental results reveal that the brine permeability in sandstone can be reduced significantly up to 7 and 40 times respectively for parallel and perpendicular beddings in this study compared to no-bedding types.