There are described herein methods and systems for operating an electric motor of a watercraft. In one method, the electric motor of the watercraft is controlled based on commands received from an accelerator of the watercraft, a sensor signal is received from at least one sensor of the watercraft while the electric motor is in operation, the sensor signal indicative of an undesirable condition of a water intake of the watercraft, and a change is effected to the controlling of the electric motor in response to receiving the sensor signal.