A filter assembly for an aquarium has a self-cleaning filter. A fine mesh filter screen is disposed between an inlet and an outlet for filtering solid matter from the water that is pumped from the aquarium, through the filter, and back to the aquarium. When the filter screen is sufficiently loaded, or according to a set schedule, the solid matter is suctioned off the filter screen with a vacuum assembly. For that purpose, the water flow is first diverted, the filter screen is rotated, and the vacuum assembly is turned on. After the screen has been vacuumed, the vacuum assembly is once more turned off and the water flow is redirected to pass through the filter screen.