The Visakhapatnam port, India is a major natural port, situated in between the Kolkata and Chennai on the East Coast and in terms of latitude and longitude its location is 17.6856° N, 83.2160° E has experienced an extreme wave oscillations 2.0 to 6.0 m in the midst of its severe weather events. In this paper numerical studies are performed to analyze the frequency distribution over the oceanic surface of standing waves in Visakhapatnam port at four respective synthetic record stations in presence of partially reflecting harbor. The convergence study is conducted to obtain the numerical accuracy of the scheme and simulation results are validated with the available studies experimentally from Ippen and Goda (1963) and Lee (1971) also with the analytical approximations. Further, the spectral density is determined corresponding to the wave period for the incident waves striking with several directions towards the Visakhapatnam port at four different record stations. The computation of the resonant frequencies is conducted in the Visakhapatnam port to examine the safe locations for the moored ship.