Wave structure interaction problem having structure over an arbitrary bottom is analyzed for its solution. The associated boundary value problem is handled using boundary element method. The associated boundary value problem converts into integral equation over the physical boundaries using this method. The physical boundaries are discretized into a finite number of elements and hence the integral equation gives rise to a system of linear algebraic equations. Finally, on solving the system of equations,  the physical quantities, namely, the reflection and transmission coefficients are obtained. For ensuring the correctness of these physical quantities, the energy balance relation is derived and verified. The present results are also verified by comparing the results available in the literature. The present study reveals that the width and height of the structure along with the undulated seabed play an important role to construct an effective wave barrier to protect various marine facilities from wave attack and also helpful to create the tranquility zone on the lee side of the structure.