In order to monitor the contamination of groundwater due to unplanned release of radioactive materials and the spread to off-site environments, the nuclear power plants (NPPs) conduct groundwater monitoring program (GWMP) in Korea. The GWMP should be established based on the groundwater flow model reflecting the conceptual site model (CSM) of the NPP’s site. In this study, in order to optimize the GWMP, the existing CSM and the groundwater flow model of the domestic NPPs site was updated by reflecting the latest groundwater level. As part of the CSM improvement, the hydrogeological units were subdivided more detailed from three to six through the review of hydrogeological characteristics of the NPPs site. In addition, major variables that affect groundwater flow, such as water conductivity, have been updated. The groundwater flow model was revised overall as the CSM was improved. In particular, the excavation depth of the structure and backfill area generated during the construction stage of the NPP structures was accurately reflected, and the drainage boundary conditions were realistically reflected. To verify the revised groundwater flow model, steady-state correction was performed using the groundwater level measured in April, 2021. As a results of the steady-state correction, the standard error of estimate, root mean square (RMS), normalized RMS, and the correlation coefficient were 0.32 m, 1.692 m, 5.608%, and 0.964, respectively. This means that the groundwater flow model is reasonably constructed. The CSM and groundwater flow model improved in this study will be used to optimize the monitoring location of groundwater in NPPs.