This paper describes a position-control algorithm for the buffer of a deep-sea mining system. The buffer is connected to a surface vessel by means of a long slender pipe on its top and to a collector on sea floor through a flexible hose at the bottom. A mathematical modeling is established for designing the controller for thrusters of the buffer, in which the dynamic response of the long pipe is taken into account. In this paper, the dynamic response is estimated by the mode superposition method and the fluid loading acting on the pipe is computed by using Morisons formula. For simplicity, the reaction from the flexible hose is not included and only the lateral motion is considered. The control algorithm is based on the PID control method. In order to guide the buffer to react only to the low-frequency motion of the surface vessel, the FIR digital filter is introduced. It can be shown numerically that the high-frequency component of ships motion can be successfully filtered out by using the FIR low pass filter.