AbstractUnderstanding the wettability of porous materials is important to model fluid flow in the subsurface. One of the critical factors that influences wetting in real reservoirs is the composition of geologic materials. The wetting properties for clay minerals can have a particularly strong impact on flow and transport. In this work, we analyze the chemical composition of a Mt. Simon sandstone core to resolve the microscopic structure of clay regions and assess how alterations to the local wetting properties influence multiphase transport based on core flooding experiments and relative permeability simulations. We show that whichever fluid has greater affinity toward clay minerals will tend to accumulate within these high surface area regions, leading to dramatic shifts in the relative permeability. This work establishes the essential importance of the mineral composition and associated wetting properties in the modeling of flow and transport in reservoir‐scale systems.