A numerical and experimental analysis of the wave overtopping over emerged and submerged structures, is presented. An original model is used in order to simulate three-dimensional free surface flows. The model is based on the numerical solution of the motion equations expressed in an integral form in time-dependent curvilinear coordinates. A non-intrusive and continuous-in-space image analysis technique, which is able to properly identify the free surface even in very shallow waters or breaking waves, is adopted for the experimental tests. Numerical and experimental results are compared, for several wave and water depth conditions.