Improved network flow models require the incorporation of increasingly accurate geometrical characterization of the microscale pore structure as well as greater information on fluid–fluid interaction (interfaces) at pore scales. We report on three dimensional (3D) pore scale medium characterization, absolute permeability computations for throat structures, and pore scale residual fluid distribution in a Berea core. X-ray computed microtomography combined with X-ray attenuating dopants is used to obtain 3D images of the pore network and to resolve phase distributions in the pore space. We present results on pore characterization, including distributions for pore volume, pore surface area, throat surface area, and principal direction diameters for pores and throats. Lattice Boltzmann computations are used to predict absolute permeabilities for individual throats reconstructed from the images. We present results on oil and water distribution in the pore space at residual conditions. We also consider the effects on residual fluid distribution due to the injection and gelation of a water-based gel. In extensive studies of Berea cores it has been observed that introducing water-based gels in the displacement process reduces permeability to water more than to oil. Our results provide supporting evidence for the involvement of gel compaction (dehydration) and oil trapping, while discounting gel blockage in throats, as mechanisms contributing to this effect.