As a precaution measure a boundary element model is applied to the future expansion deployment of Taipei Harbor to examine resonance phenomena. The boundary element model is developed based on linear wave theory of constant water depth, and solving for the Helmholtz equation. Three major incident wave directions, namely, NNE, N, and WNW, together with a broad spectrum of wave periods are considered. Realistic reflecting conditions on the problem boundaries are implemented in the calculation, so that numerical results reflect actual resonant wave frequencies. In order to clarify if resonant frequencies calculated numerically do exist, the in-situ observatory wave data, in particular typhoon wave, are also analyzed. From the present study, wave distribution inside Taipei Harbor for specific incident wave and direction, and variation of wave amplification versus wave period are obtained. With the considered wave reflecting condition, wave resonance seldom occurs within Taipei Harbor. However, at location of recreational boat berthing area resonance results are obvious. It is suggested that mitigation measures should be considered for safety reason.