A nonlinear numerical model based on depth averaged equations and a relevant physical model have been investigated for the deformation of the water wave propagating over a submerged parabolic obstacle in the presence of uniform current. Physical and numerical modeling for wave with both following and opposing currents are done to explore the wave evolutions during passage over the submerged obstacle. A third-order Stokes dispersion relation is utilized in some cases in the computation. Separated flow zone is taken into consideration by two empirical equations obtained from the physical model testing done by the authors. Verification and validation of the numerical model by other published theoretical and experimental data are presented.