The basic principles of geological risk calculation through probability of success (PoS) are mostly applied to numerical estimation of additional hydrocarbon existence in proven reservoirs or potential hydrocarbon discoveries in selected geological regional subsurface volumes. It can be adapted and validated for a comprehensive input dataset collected in the selected petroleum province, by dividing up geological events into several probability categories and classes. Such methodology has been widely developed in the last decades in the Croatian subsurface—mostly in the Croatian Pannonian Basin System (CPBS). Through the adaptation of geological categories, it was also applied in hybrid, i.e., stochastic, models developed in the CPBS (Drava Depression), mostly for inclusion of porosity values. As the robustness of this methodology is very high, it was also modified to estimate the influence of water-flooding in increasing oil recovery in some proven Neogene sandstone reservoirs in the CPBS (Sava Depression). This new modification is presented to be applied to geological risk calculation, intending to assess the safety of geological environment storage in deep wells, where spent nuclear fuel (SPN) would be disposed, a subject of great importance. The conceptual study encompassed the magmatic and metamorphic rocks in the pre-Neogene basement of the CPBS, intended to be used for such purpose. Regionally distributed lithologies are considered for nuclear waste disposal purpose, in order to detect the safest ones, considering petrophysical values, water saturation, recent weathering and tectonic activity.