The flow properties of carbonate reservoir rocks depend on the pore and throat shape (geometry), the way they are interconnected (topology) and on the forces associated with the fluid-rock interactions (wettability). Little quantitative information on these parameters and their dependencies are currently available. We present the preliminary results of an on-going multiscale study of carbonate rocks which integrates classical diagenetic characterization of their pore system with 3D visualization and analysis of its structure (from micro-CT imaging) and mineral and elemental surface composition (from QEMSCAN). Tomograms of carbonate cores and minicores were obtained with our in-house micro-CT scanners, which allow us a spatial resolution down to the order of 1 μm. Macroporosity, microporosity and pore networks were extracted by image processing and analysis using the MANGO software. These same cores and minicores were then sectioned for 2D maps of their mineral composition to be acquired by QEMSCAN and subsequently spatially registered into the corresponding 3D tomogram. In addition to this analysis of carbonate samples in their dry state, minicores were also prepared and micro-CT imaged in a series of wet states after saturation, drainage, aging and spontaneous imbibition. This facilitated visualization and quantification of the pore-scale changes in saturation during these processes. The observations will help to guide the further development of modelling and simulation of multiphase flow in carbonates to predict and enhance the recovery of oil.