Disposal of hazardous non-radioactive wastes is a major problem because of our incomplete understanding of subsurface processes. We are forced to simplify with models and thus to overlook some of the natural defects in real storage sites. The aim of this paper is to provide a conceptual framework and to discuss some examples of previously overlooked processes leading to leakage in storage sites. In the late seventies the hydrogeologic methodology and the governmental regulatory guidelines were insufficient to prevent contamination of groundwater and atmospheric pollution. Frequently, engineers dealt with the bulk properties of rocks and grossly underestimated the influence of the 3-D flow system due to the variable interconnections between permeable zones and the heterogeneous mineralogical and sedimentological character of the media under consideration.