To study the influence of ship’s berthing and departing operation in the mixed waters on its navigable efficiency, we establish the marine traffic flow volatility model in mixed areas based on traffic wave theory and combining with the traffic flow characteristics of the ship to explain further the vessel traffic flow gathering and dissipating process during berthing and departing operations. According to the vessel traffic volume, speed, the current density of the ship and relying on the time from the mooring operations, we establish the mixed- water interference range & time model. Taking the Fujiangsha south channel for example, we carry out a research on the vessel navigation efficiency in mixed waters under the safe condition.