We derive a Hamiltonian formulation for two-dimensional nonlinear long waves between two bodies of immiscible fluid with a periodic bottom. From the formulation and using the Hamiltonian perturbation theory, we obtain effective
Boussinesq equations that describe the motion of bidirectional long waves and unidirectional equations that are similar to the KdV equation for the case in which the bottom possesses short length scale. The computations for these results are performed in the framework of an asymptotic analysis of multiple scale operators.