This paper presents a new approch in the design of output feedback control system based on disturbance observer for dynamic positioning vessels. The proposed control system includes a controller and a structure of a modified notch filter and a nonlinear observer. The filter is used for estimating low-frequency motions and removing the wave-frequency motions by using vessel position mesurement. The low-frequency disturbances and vessel-velocites are estimated in nonliner observer using the low-frequency vessel motion. In this structre, wave filtering and low-frequency motion estimation are independent from the estimation of low-frequency disturbances and vessel velocities. It causes to incease the accuracy of filtering and estimation which results in desirable performance of control system. Also, filtering is independent of the vessel and low frequency disturbances models, and therefore it is not affected by modeling uncertainty. The effect of wave filtering and low-frequency disturbances estimation in DP control system from the point of reducing control signal flactutions were evaluated with numerical simulation. This is important in view of reduction of wear and tear in propaltion system and fuel consumption in a surface vessel. Futhermore, simulation results show that the proposed method has better performances in comparision with conventional method.