Geosynthetic clay liners and compacted clay liners are common bottom barriers in landfills. One of the important steps in barrier design is to evaluate the effectiveness of the bottom barrier system in practical conditions based on modelling contaminant migration. This study simulates the migration of ammonium ions through proposed bottom barriers for design under consideration of the southern Hanoi area’s temperature and geohydrology conditions, then evaluates potential impacts on normalized ammonium concentration in groundwater. Proposed bottom barriers include geosynthetic clay liner and compacted clay liner constituting from local soils. The results indicated the reclamation of locally natural soils and geosynthetic clay liner (GCL) placement was approximately 5.2 and 13.4 times more effective in slowing ammonium migration than natural soil, respectively. Compacted clay liner of natural soils exhibited few impacts from elevated temperature. However, being sensitive to an elevated temperature at 50°C, the barrier performance of GCL caused the peak normalized ammonium concentration in groundwater to be 4.2 times higher than normal conditions. Notably, normalized ammonium concentration in groundwater increased 29 times when the geosynthetic clay liner was exposed to 2 dry-wet cycles with ammonium solution. These results provided useful references for designers and engineers to consider in selecting barrier materials in the new landfill.