Abstract The AP1000 Passive Residual Heat Removal (PRHR) system plays a significant role as it helps to remove the core decay heat, using the In-containment Refueling Water Storage Tank (IRWST) as a heat sink. The IRWST is located above the core, promoting natural circulation and allowing to be the mid-term heat-sink for the reactor core. The thermo-hydraulic pool behavior during an accident has an influence in the containment pressure and temperature, as happens in the pressure suppression pool in BWR reactors. Due to the importance of the IRWST performance on the AP1000 containment, a numerical analysis of a scaled experiment has been done using the GOTHIC code. Firstly, an IRWST scaled-down model is created, a mesh sensitivity analysis is performed, and the results obtained are compared against experimental results available in the literature. It is found the importance of the mesh discretization for the proper thermal-stratification modeling. Then, the reference model setup and mesh are applied in a full-scale prototypic model. The mesh influence on the thermal stratification is analyzed, as well as its impact on the AP1000 containment pressure. The mesh and setup for the full-scale model are selected to be implemented in a full containment 3D model in future works.