An innovative self-elevating seawall is attracting attention as an effective countermeasure to protect ports and their hinterland from tsunamis. However, seawater may intrude into the port basin through a narrow gap between its gate units, resulting in a significant water level change when a tsunami strikes. Herein, a 2D–3D hybrid hydrodynamic model is used to investigate water inflow through the gap in a self-elevating seawall, induced by a tsunami that approaches a port. A practical hydraulic head-to-discharge formula is then derived. This formula is validated by a case analysis that numerically simulates the intrusion with a hypothetical time series of water levels originating from a tsunami and astronomical tide. A self-elevating seawall acts as an effective low-pass filter system, though it may not completely prevent inflow. A case study for assessing a medium sized fishery port also demonstrates that tsunami-induced impact can be significantly reduced by sheltering with the self-elevating seawall system. However, a longer wave component, such as astronomical tide, will inevitably intrude into the port through the gate gap as well as the void of breakwater's rubble mound as seepage flow. The risk of a secondary tsunami, gate-opening-induced tsunami, is also addressed for appropriate gate operations after a tsunami has receded. The proposed model can calculate rise/fall in water level over a port basin enclosed by the self-elevating seawall and port breakwaters using a simple spreadsheet without expensive computational fluid dynamics.