A pump-jet works by having an intake (usually at the bottom of the hull) that allows water to pass underneath the vessel into the engines. Water enters the pump through this inlet. The pump can be of a centrifugal design for high speeds, an inducer for low speeds, or an axial flow pump for medium speeds. The water pressure inside the inlet is increased by the pump and forced backwards through a nozzle. With the use of a reversing bucket, reverse thrust can also be achieved for faring backwards, quickly and without the need to change gear or adjust engine thrust. The reversing bucket can also be used to help slow the ship down when braking. This feature is the main reason pump jets are so maneuverable.

The nozzle also provides the steering of the pump-jets. Plates, similar to rudders, can be attached to the nozzle in order to redirect the water flow port and starboard. In a way, this is similar to the principles of air thrust vectoring, a technique which has long been used in military jet-powered aircraft. This provides pumpjet-powered ships with superior agility at sea. Another advantage is that when faring backwards by using the reversing bucket, steering is not inverted, as opposed to propeller-powered ships.

Pump-jet powered watercraft do suffer from the Coandă effect, which must be taken into account when making changes in heading. The heading needs to be adjusted two degrees further than what would normally be required because of this effect.