Underground hydrogen storage (UHS) technology promotes large-scale energy storage and balancing of energy grids due to mismatch between renewable energy production and demand patterns. As this technology is significantly dependent on the use of subsurface porous rocks for hydrogen storage, an adequate understanding of the porous media properties and flow behaviour of hydrogen is crucial for implementing UHS. Modelling porosity and permeability is vital for understanding storage and fluid flow in porous geological media such as depleted hydrocarbon reservoirs and saline aquifers. Porosity and permeability depend on the size, shape and connectivity of the pores, making modelling of pore-scale properties a challenging task in the GEOZeit project to investigate the suitability of potential sandstone formations in Germany for UHS. This work presents a pore scale Finite Element Modelling (FEM) using scanning electron microscopy (SEM) images of Bentheimer sandstone to evaluate critical reservoir properties like porosity and permeability in tandem with fluid properties and in-situ reservoir conditions, and allows the comparison with measured experimental values. The model is implemented in COMSOL Multiphysics software using the creeping flow interface which computes permeability based on Darcy’s law. The production rates of different fluids (hydrogen, nitrogen, methane, carbon-dioxide and water) were determined based on the evaluated porosity and permeability from the Bentheimer SEM image. The result of the integration of SEM scanning and computational methods to model porosity and permeability offers more insight into understanding the complexity of fluid flow in porous media for accurate assessment of the subsurface before and during UHS operations.