A three-dimensional reservoir simulator used for automated upscaling relative permeability and capillary pressure in multi-porosity systems comprising disparate rock-types. A coarse-scale single-porosity model incorporating multi-porosity model properties may be derived from a fine-scale single-porosity model based, at least in part, on simulation of a model comprising data from one or more regions of interest. Real-world and laboratory measurements of the one or more regions of interest may be provided to the fine-scale single-porosity simulation model and the fine-scale single-porosity model may be subjected to one or more fractional flow simulation processes and one or more displacement simulation processes. The fine-scale model properties may be modified based, at least in part, on the results of the one or more fractional flow simulation processes and one or more displacement simulation processes. Coarse scale-model properties may be derived from the fine-scale single-porosity model properties by upscaling the fine-scale single-porosity model. The coarse-scale single-porosity simulation model incorporating multi-porosity model properties may be used to improve operational decision-making, including drilling operations and reservoir management.