A mathematical model has been developed to analyze the influence of extreme water waves over multiconnected regions in Visakhapatnam Port, India by considering an average water depth in each multiconnected regions. In addition, partial reflection of incident waves on coastal boundary is also considered. The domain of interest is divided mainly into two regions, i.e., open sea region and harbor region namely as Region-I and Region-II, respectively. Further, Region-II is divided into multiple connected regions. The 2-D boundary element method (BEM) including the Chebyshev point discretization is utilized to solve the Helmholtz equation in each region separately to determine the wave amplification. The numerical convergence is performed to obtain the optimum numerical accuracy and the validation of the current numerical approach is also conducted by comparing the simulation results with existing studies. The four key spots based on the moored ship locations in Visakhapatnam Port are identified to perform the numerical simulation. The wave amplification at these locations is estimated for monochromatic incident waves, considering approximate water depth and different reflection coefficients on the wall of port under the resonance conditions. In addition, wave field analysis inside the Visakhapatnam Port is also conducted to understand resonance conditions. The current numerical model provides an efficient tool to analyze the amplification on any realistic ports or harbors.