A reference scenario of vault safety case prepared by the IAEA for the near-surface disposal facility of low-and informed]ate-level radioactive wastes is assessed with the MASCOT program. The appropriate conceptual models for the MASCOT implementation is developed. An assessment of groundwater pathway through a drinking well as a geosphere-biosphere interface is performed first. then biosphere pathway is analysed to estimate the radiological consequences of the disposed radionuclides based on compartment modeling approach. The validity of conceptual modeling for the reference scenario is investigated where possible comparing to the results generated by the other assessment. The result of this study shows that the typical conceptual model for groundwater pathway represented by the compartment model ran be satisfactorily used for safety assessment of the entire disposal system in a cons]stent way. It is also shown that safety assessment of a disposal facility considering complex and various pathways would be possible by the MASCOT program.