A watercraft maneuvering system includes an actuator having a function of generating a propulsion force of a watercraft and a function of causing the watercraft to generate a moment, an operation unit configured to receive an input operation of a watercraft operator, and a watercraft control device configured to operate the actuator. When the operation unit has received an input operation for stopping an operation of the actuator while the watercraft control device is operating the actuator, the watercraft control device operates the actuator without any need for the operation unit to receive the input operation for at least one function of the actuator generating the propulsion force in an opposite direction to a direction of an inertial force occurring in the watercraft and causing the watercraft to generate the moment in an opposite direction to a direction of a moment of inertia occurring in the watercraft.