SUMMARYWe introduce a new method to discretize inclined non-planar two-dimensional (2D) fractures in threedimensional (3D) fractured media for subsurface flow and transport simulations. The 2D fractures are represented by ellipsoids. We first discretize the fractures and generate a 2D finite element mesh for each fracture. Then, the mesh of fractures is analyzed by searching and treating critical geometric configurations. Based on that search, the method generates a quality mesh and allows for including finer grids. A solute transport problem in fractured porous media is solved to test the method. The results show that the method (i) adequately represents the fractured domain by maintaining the geometric integrity of input surfaces and geologic data, (ii) provides accurate results for both simple and complex fractured domains, (iii) is insensitive to spatial discretization, and (iv) is computationally very efficient. For inclined and vertical fractures, analytical and numerical solutions are shown to be in good agreement. The method is therefore suitable to discretize fracture networks for flow and transport simulations in fractured porous media.