A semi-analytical method for upscaling two-phase immiscible flows in heterogeneous porous media is described. This method is developed for stratified reservoirs with perfect communication between layers (the case of vertical equilibrium), in a viscous dominant regime, where the effects of capillary forces and gravity may be neglected. The method is discussed on the example of its basic application: waterflooding in petroleum reservoirs. We apply asymptotic analysis to a system of two-dimensional (2D) mass conservation equations for incompressible fluids. For high anisotropy ratios, the pressure gradient in vertical direction may be set zero, which is the only assumption of our derivation. In this way, the 2D Buckley–Leverett problem may be reduced to a one-dimensional problem for a system of quasi-linear hyperbolic equations, of a number equal to the number of layers in the reservoir. They are solved numerically, based on an upstream finite difference algorithm. Self-similarity of the solution makes it possible to compute pseudofractional flow functions depending on the average saturation. The computer partial differential equation solver COMSOL is used for comparison of the complete 2D solutions with averaged 1D simulations. Cases of both discrete and continuous (log-normal) permeability distribution are studied. Generally, saturation profiles of the 1D model are only slightly different from the 2D simulation results. Recovery curves and fractional flow curves fit well. Calculations show that at a favorable mobility ratio (displaced to displacing phase) crossflow increases the recovery, while at an unfavorable mobility ratio, the effect is the opposite. Compared with the classical Hearn method, our method is more general and more precise, since it does not assume universal relative permeabilities and piston-like displacement, and it presumes non-zero exchange between layers. The method generalizes also the study of Yortsos (Transp Porous Media 18:107–129, 1995), taking into account in a more consistent way the interactions between the layers.