Assessing long-term performance of geologic repositories requires simulation of flow through heterogeneous geologic formations. The effect on flow field of discontinuities such as fracture zones in such media is not only of interest to waste management professionals but also to those involved in petroleum engineering and water resources development. Significant differences in the space and time scales associated with these discontinuities as compared with those associated with bulk geology cause special problems in modeling. The modeling problems are in addition to the very practical problem inherent in proper topological characterization of the discontinuities and also in field measurement of their flow and transport properties. After briefly reviewing various generally used classes of methods for accommodating heterogeneities represented by fractures in numerical models, a different technique of deriving mass balance equations in the presence of fractures is discussed. Compared with full representation of fractures, the proposed technique provides coarser resolution of the flow field, but it is relatively computationally efficient. Two examples of its application are also provided.