In this paper, a stabilized incompressible smoothed particle hydrodynamics (ISPH) method is presented in three dimensions for simulating fluid flows through porous structures. In the ISPH algorithm, a semi-implicit velocity correction procedure is utilized and the pressure is implicitly evaluated by solving pressure Poisson equation. Evaluated pressure has been improved by relaxing the density invariance condition to formulate a modified pressure Poisson equation. The effect of eddy viscosity by using a sub-particle scale turbulence model is introduced to the entire computational domain. The key point for the application to the non-Darcy flows is to include porosity and drag forces of the medium into ISPH method. Modified density of particles according to their porosity is introduced to satisfy continuity criteria in ISPH method. Tracking free surface with Dirichlet boundary condition is modified for the free surface flows in the porous structure. In this study, different numerical tests for fluid flows through porous structures have been simulated. Also, the results from this investigation are well validated and have favorable comparisons with the experimental results.