A novel mathematical model formulation based on spectral boundary element method (SBEM) is presented to examine the wave response in the Pohang New Harbor (PNH), South Korea and Paradip port, Odisha, India. In SBEM, the boundary element method (BEM) is coupled with the spectral element method (SEM) to enhance the numerical accuracy of the present numerical scheme. The numerical solution on each boundary element is obtained by using boundary integral associated with Chebyshev point discretization. The boundary Integrals are transformed using Jacobians and evaluated with Clenshaw Curtis Quadrature rule. Convergence analysis is performed on rectangular domain for present scheme, BEM and hybrid finite element method (HFEM), which shows that the present numerical scheme is better as compared to other traditional numerical schemes. Further, the simulation results are validated with BEM, analytical method and experimental data from Lee (1971) and Ippen and Goda (1963). The wave amplification is obtained at six record stations inside the PNH, South Korea and Paradip port, Odisha, India. In addition, the spectral density is also determined for multidirectional random waves propagating towards the PNH and Paradip port at the same record station. The resonant frequencies are estimated in PNH and Paradip port for the safe navigation of moored ship.