The pore structure of many carbonate formations is known to be very complex and heterogeneous. Heterogeneity is manifested by the presence of different types, sizes, and shapes of pores resulting from sedimentation and diagenetic actions. These complexities greatly increase uncertainties in estimated rock hydraulic properties in that different permeability values may occur for samples having similar porosities. In order to understand the effects of pore structure and heterogeneity, petrophysical analyses were performed on coquina samples from the Morro do Chaves Formation (Barremian, Sergipe-Alagoas Basin), which is an analogue of Brazilian Pre-salt oil reservoirs of Itapema Formation in the Santos Basin. Routine core analyses, and NMR and MICP measurements were carried out to obtain pore body and pore throat distributions. ObtainedT(2) relaxation times were converted to pore size radii by matching the NMR and MICP curves. Pore-scale imaging and pore network modelling were performed using microCT scans and the PoreFlow software, respectively. Calculated permeabilities using PoreFlow showed excellent agreement with the routine laboratory measurements. Samples having pore bodies with a higher coordination number showed much larger permeabilities at similar porosities. This study includes a statistical analysis of various features that caused the observed differences in permeability of the coquinas, including the role of connectivity of the entire porous system. Limitations and challenges of the various techniques, and the imaging and pore-scale flow simulations, are discussed.