In the last decade, the fundamental understanding of pore-scale flow in porous media has been undergoing a revolution through the recent development of new pore-scale imaging techniques, reconstruction of three-dimensional pore space images, and advances in the computational methods for solving complex fluid flow equations directly or indirectly on the reconstructed three-dimensional pore space images. Important applications include hydrocarbon recovery from - and CO2 storage in - reservoir rock formations. Of particular importance is the consideration of carbonate reservoirs, as our understanding of carbonates with respect to geometry and fluid flow processes is still very limited in comparison with sandstone reservoirs. This thesis consists of work mainly performed within the Qatar Carbonates and Carbon Storage Research Centre (QCCSRC) project, focusing on development of three dimensional imaging techniques for accurately characterizing and predicting flow/transport properties in both complex benchmark carbonate and sandstone rock samples. Firstly, the thesis presents advances in the application of Confocal Laser Scanning Microscopy (CLSM), including the improvement of existing sample preparation techniques and a step-by step guide for imaging heterogeneous rock samples exhibiting sub-micron resolution pores. A novel method has been developed combining CLSM with sequential grinding and polishing to obtain deep 3D pore-scale images. This overcomes a traditional limitation of CLSM, where the depth information in a single slice is limited by attenuation of the laser light. Other features of this new method include a wide field of view at high resolution to arbitrary depth; fewer grinding steps than conventional serial sectioning using 2D microscopy; the image quality does not degrade with sample size, as e.g. in micro-computed tomography (micro- CT) imaging. Secondly, it presents two fundamental issues - Representative Element of Volume (REV) and scale dependency which are addressed with qualitative and quantitative solutions for rocks increasing in heterogeneity from beadpacks to sandpacks to sandstone to carbonate rocks. The REV is predicted using the mathematical concept of the Convex Hull, CH, and the Lorenz coefficient, LC, to investigate the relation between two macroscopic properties simultaneously, in this case porosity and absolute permeability. The effect of voxel resolution is then studied on the segmented macro-pore phase (macro-porosity) and intermediate phase (micro-porosity) and the fluid flow properties of the connected macro-pore space using lattice-Boltzmann (LB) and pore network (PN) modelling methods. A numerical coarsening (up-scaling) algorithm have also been applied to reduce the computational power and time required to accurately predict the flow properties using the LB and PN methods. Finally, a quantitative methodology has been developed to predict petrophysical properties, including porosity and absolute permeability for X-ray medical computed tomography (CT) carbonate core images of length 120 meters using image based analysis. The porosity is calculated using a simple segmentation based on intensity grey values and the absolute permeability using the Kozeny-Carman equation. The calculated petrophysical properties were validated with the experimental plug data.