This study investigates the scattering of surface ocean waves by a submerged viscoelastic plate placed over the variable bottom topography under the assumptions of linear theory. The solution is derived using the hybrid boundary element method. The boundary element method is faster and easier to use when compared to the most widely used analytical method, such as the eigenfunction expansion method. Moreover, the application of analytical methods is restricted to structures with regular geometries and flat sea bottom. However, the present solution technique works for the plate at any angle placed over the variable bottom topography. Furthermore, as a particular case, the scattering problem is analyzed when a rigid wall is placed downstream. Energy balance relations are derived to check the accuracy of the computed numerical results. The effect of sinusoidally varying bottom topography, damping parameter, and plate edge conditions on the Bragg resonance phenomenon is analyzed. Initially, the solutions are presented in the frequency domain using the hybrid boundary element method and then extended to the time domain using the Fourier transform. It is observed that when the edges of the submerged plate are fixed, the Bragg resonance occurs at lower values of the frequency parameter. However, the Bragg resonance occurs around the primary Bragg value when the plate has free edges. For certain incident wave frequencies, the viscoelastic plate that completely covers the undulating bed dissipates a greater amount of wave energy than when the plate only partially covers the seabed.