In a method for calibrating a system for controlling thrust and steering of a drive arrangement in a watercraft, the system includes an operating device adapted for indicating a requested direction of travel of the watercraft, the operating device being connected to a control unit for providing corresponding thrust and steering commands to the drive arrangement. The method includes receiving an activation command in the control unit, for beginning the calibration, detecting any movements of the operating device, storing values corresponding to the movements in the control unit together with corresponding thrust and steering values, and repeating the detecting step and the storing step until a termination command is received in the control unit, thereby using the stored values in subsequent operation of the operating device for indicating the direction of travel of the watercraft. An arrangement for calibrating a system for controlling thrust and steering of a drive arrangement in a watercraft is also provided.