Fluid flow in porous media is important for a number of fields including nuclear waste disposal, oil and gas, fuel cells, water treatment and civil engineering. The aim of this work is to improve the current understanding of how the pore space governs the fluid flow in porous media in the context of nuclear waste disposal. The effects of biofilm formation on flow are also investigated. The thesis begins with a review of the current porous media characterisation techniques and the means for converting the pore space into pore network models and their existing applications. Further, I review the current understanding of biofilm lifecycle in the context of porous media and its interactions with fluid flow. The model porous media used in this project is Hollington sandstone. The pore space of the material is characterised by X-ray CT and the equivalent pore networks from two popular pore network extraction algorithms are compared comprehensively. The results indicate that different pore network extraction algorithms could interpret the same pore space rather differently. Despite these differences, the single-phase flow properties of the extracted networks are in good agreement with the estimates from a direct approach. However, it is recommended that any flow or transport study using pore network modelling should entail a sensitivity study aiming to determine if the model results are extraction method specific. Following these results, a pore merging algorithm is introduced aimed to improve the over segmentation of long throats and hence improve the quality of the extracted statistics. The improved model is used to study quantitatively the pore space evolution of shale rock during pyrolysis. Next, the extracted statistics from one of the algorithms is used to explore the potential of regular pore network models for up-scaling the flow properties of porous materials. Analysis showed that the anisotropic flow properties observed in the irregular models are due to the different number of red (critical) features present along the flow direction. This observation is used to construct large regular models that can mimic that behaviour and to discuss the potential of estimating the flow properties of porous media based on their isotropic and anisotropic properties. Finally, a long-term flow-through column experiment is conducted aiming to understand the effects of bacterial colonisation on flow in Hollington sandstone. The results show that such systems are quite complex and are susceptible to perturbations. The flow properties of the sandstone were reduced significantly during the course of the experiment. The possible mechanisms responsible for the observed reductions in permeability are discussed and the need for developing new imaging techniques that can allow examining biofilm development in-situ is underlined as necessary for drawing more definitive conclusions.