The natural frequencies of different areas in Dayaowan harbor are obtained by the Boussinesq numerical wave model.Simulating the surface responses of the whole water to incident irregular waves,we get the results that a small spectrum peak period of irregular wave can induce local low frequency fluctuations after a certain time by wave energy transfers from high frequency to the lower in the local areas of Dayaowan harbor.The incident of the waves can only stimulate the local water resonances such as in the bottom of the harbor and in the small harbor in the south bank,but not in the whole harbor.It is effective to reduce fluctuations in local waters with the measure for decreasing the reflection coefficient of the borders.