Simulation by a finite volume method of the transfer by water of radioactive elements in sites of nuclear waste storage, on large time and space scales, is the only possible way to analyze the safety of disposal. To properly represent the different pathways of radionuclides, surface topography (valleys, reliefs, rivers), geologic layers and simplified storage facilities must be accurately modeled. This paper proposes a new methodology for generating hex-dominant meshes (well suited for a finite volume formulation) of geologic structures complying with these different geometric constraints. First, a reference 2D domain is obtained by projecting all the line constraints into a horizontal plane. Different size specifications are given for workings, outcrop lines and rivers. Using an adaptive methodology, the size variation is bounded by a specified threshold in order to obtain a high quality quad-dominant mesh. Secondly, a hex-dominant mesh of the geological medium is generated by a vertical extrusion. Depending on the configuration of the surfaces found (interfaces between two layers, top or bottom faces of underground workings), hexahedra, prisms, pyramids and tetrahedra are generated. The generation of volume elements follows a global order established on the whole set of surfaces to ensure the conformity of the resulting mesh. An example of mesh construction of a geologic structure will illustrate the suitability of the proposed methodology.