The primary objective was to predict the relative storage capacity of carbonate rocks relevant for carbon dioxide sequestration. To achieve this, a detailed pore scale characterization of model carbonate rocks, Indiana Limestone and Pink Dolomite, was conducted utilizing micro-computed tomography (microCT) data using pore network modeling and invasion percolation simulations. For the first time in literature, Pink Dolomite’s pore space characteristics were analyzed. A secondary objective was to compare thresholding techniques as applied to carbonates which exhibit dual porosity (porosity at multiple length scales). The analysis showed the sensitivity of existing methods to the thresholding technique, imaging method and material. Overall, the contributions of this work provide an assessment of two carbonates relevant for carbon capture and storage at the pore scale;​ and a preliminary assessment into thresholding dual porosity carbonates.