Water inflow following a collision or grounding accident leading to the opening of a (group of) compartment(s) to the sea, may put at risk the safety of the persons on board and the environment. Sophisticated numerical tools are required to simulate the flow of the floodwater and the resulting response of the damaged ship to obtain a better understanding of the relevant phenomena. A novel method to perform flooding simulations is presented in this work, where the high-fidelity Smoothed Particle Hydrodynamics (SPH) method is employed for the simulation of the flow inside the flooded compartment, while the flow around the ship is considered based on potential theory assumptions. This decomposition of the problem targets to a reasonable compromise between accuracy and computational cost, since the computationally demanding SPH method is utilized exclusively for the solution of the smaller domain inside the damaged compartment, where intense dynamic phenomena are anticipated.