Salinity intrusion is one of the most pressing threats to unconfined coastal aquifers, and its simulation is of great importance for groundwater research and management. This study compared the performances of two computational fluid dynamics (CFD) software applications, ANSYS Fluent 2022 R2 and COMSOL Multiphysics 5.6, in simulating the transport of saltwater in a pilot-scale experimental setup, which was built to recreate two boundary conditions of unconfined aquifers with homogeneous stratigraphy. The experiments were performed until the saline wedge reached a quasi-steady-state condition. Sequential photographs and image analysis were required to record the movement of the saline toe and the saline wedge location. The maximum toe length was achieved under the head-controlled boundary condition, with a toe length of 1.6 m after 7 h of the experiment, and 1.65 m and 1.79 m for the COMSOL and ANSYS Fluent simulations, respectively. The findings evidence that the flux-controlled condition produced a better representation of the saline wedge than the head-controlled condition, indicating good agreement between the CFD simulations and the experimental data. Recommendations for future research include CFD simulations of real coastal aquifers and coupling fluid dynamics with other processes such as land subsidence.