The intrusion of salt water into coastal regions threatens water resources, especially in arid and semi-arid regions. It damages large quantities of fresh water in these regions, and the productivity of the freshwater abstraction wells declines. Management of seawater intrusion (SWI) is therefore needed to improve fresh groundwater in these regions. This study investigated 12 different configurations of mixed physical subsurface barriers (MPBs) to control SWI in homogeneous and heterogeneous layered aquifers. The effectiveness of different MPB locations and configurations was tested, including (i) a barrier wall on the landward side and the subsurface dams on the seaward side, (ii) a barrier wall on the seaward side and a subsurface dam on the landward side, and (iii) the barrier wall was placed above the subsurface dam, both with different permeabilities. All simulations were based on the SEAWAT code. The numerical model was validated against experimental data. The results showed that a permeable cut-off wall above an impermeable subterranean dam (case MPB-3) with different permeabilities resulted in a reduction of the seawater wedge of 91% and 92% for homogeneous and heterogeneous layered aquifers, respectively. When the barrier wall was placed on the land side and the dam on the seaside (case MPB-1), the reduction of the seawater wedge reached 83% and 85% for homogeneous and heterogeneous layered aquifers, respectively. In contrast, when the dam was placed on the land side and the wall on the seaside (case MPB-2), the saltwater wedge was reduced by 73% for both homogeneous and heterogeneous layered aquifers. In addition, a case study was conducted on the Biscayne aquifer, southeast Florida, USA, with homogeneous conditions. Seawater intrusion was reduced by 36% and 44% in case MPB-1, 41% and 38% in case MPB-2, and 43% and 46% in case MPB-3. These seawater intrusion control methods offer numerous benefits, including improving freshwater storage, effectively controlling salinity during droughts, and potentially improving contaminant management.