In this study, hydraulic model experiments were conducted to measure the saltwater–freshwater equilibrium interface in a coastal aquifer with underground obstructions such as an impermeable seawall. To analyse the hydraulic characteristics inside the coastal aquifer, numerical analysis was conducted using a non-hydrostatic Navier-Stokes solver based on the Porous Body Model (PBM), which can directly analyse groundwater flow. A unique saltwater–freshwater equilibrium interface that does not appear in typical coastal aquifer analyses was observed in a sandy tank experiment. In the experiment, the rise of the groundwater level behind the seawall increased the pressure gradient and groundwater flow rate, causing the saltwater–freshwater interface to move towards the sea and a freshwater region to form on the seabed in front of the seawall. The numerical analysis enabled close examination of the groundwater level distribution, groundwater flow, seawater–freshwater interface, and pore water pressure characteristics of the coastal aquifer with underground obstructions. The sandy tank experiment also provided an understanding of the hydraulic characteristics of groundwater in the coastal aquifer with a seawall, which previously could not be accurately analysed. The experimental and analytical results demonstrated that the rise of groundwater level due to underground obstructions in the coastal aquifer increased the pressure gradient and groundwater flow rate and slowed seawater intrusion. This principle can be employed to sufficiently reduce seawater intrusion of coastal aquifers.