Because of their extreme heterogeneity at multiple scales, carbonate rocks present a great challenge for studying and managing oil reservoirs. Depositional processes and diagenetic alterations of carbonates may have produced very complex pore structures and, consequently, variable fluid storage and flow properties of hydrocarbon reservoirs. To understand the impact of mineralogy on the pore system, we analyzed four carbonate rock samples (coquinas) from the Morro do Chaves Formation in Brazil. For this study, we used thin sections and XRD for their mineralogical characterization, together with routine core analysis, NMR, MICP and microCT for the petrophysical characterizations. The samples revealed very similar porosity values but considerably different permeabilities. Samples with a relatively high quartz content (terrigenous material) generally had lower permeabilities, mostly caused by more mineral fragmentation. Samples with little or no quartz in turn exhibited high permeabilities due to less fragmentation and more diagenetic actions (e.g., dissolution of shells). Results confirm that carbonate minerals are very susceptible to diagenesis, leading to modifications in their pore body and pore throat sizes, and creating pores classified as moldic and vug pores, or even clogging them. For one of the samples, we acquired detailed pore skeleton information based on microCT images to obtain a more complete understanding of its structural characteristics.