In this paper the fundamental relationships of relative permeability and saturation are derived and expressed in simple mathematical forms in a single variable aperture fracture. The minimum entry aperture is defined to represent the minimum aperture with which the void of the fracture can be invaded by non-aqueous phase liquids (NAPLs). The effect of aperture variation on properties of two-phase flow is investigated with examples and the analytical results indicate that NAPL and water hinder each other's movement to different degrees. The presence of water in the fracture does little to hinder NAPL flow, while the presence of NAPL in the fracture results in a significant reduction of water flow. Some possible implications to site characterization and aquifer remediation are discussed.