Isolation of high-level nuclear waste in permanent geological repositories has been a major concern for over 30 years due to the migration of dissolved radio nuclides reaching the water table (10,000-year compliance period) as water moves through the repository and the surrounding area. Repositories based on mathematical models allow for long-term geological phenomena and involve many approximations; however, experimental verification of long-term processes is impossible. Countries must determine if geological disposal is adequate for permanent storage. Many countries have extensively studied different aspects of safely confining the highly radioactive waste in an underground repository based on the unique geological composition at their selected repository location. This paper discusses two computer codes developed by various countries to study the coupled thermal, mechanical, and chemical process in these environments, and the migration of radionuclide. Further, this paper presents the results of a case study of the Magma-hydrothermal (MH) computer code, modified by the author, applied to nuclear waste repository analysis. The MH code verified by simulating natural systems thus, creating the ultimate benchmark. This approach based on processes similar to those expected near waste repositories currently occurring in natural systems.