Using one-dimensional Beji & Nadaoka extended Boussinesq equation, a numerical study of solitary waves over submerged breakwaters has been conducted. Two different obstacles of rectangular as well as circular geometries over the seabed inside a channel have been considered in view of solitary waves passing by. Since these bars possess sharp vertical edges, they cannot directly be modeled by Boussinesq equations. Thus, sharply sloped lines over a short span have replaced the vertical sides, and the interactions of waves including reflection, transmission, and dispersion over the seabed with circular and rectangular shapes during the propagation have been investigated. In this numerical simulation, finite element scheme has been used for spatial discretization. Linear elements along with linear interpolation functions have been utilized for velocity components and the water surface elevation. For time integration, a fourth-order Adams-Bashforth-Moulton predictor-corrector method has been applied. Results indicate that neglecting the vertical edges and ignoring the vortex shedding would have minimal effect on the propagating waves and reflected waves with weak nonlinearity.