An aquarium cleaning system uses a housing that seals to the bottom of the aquarium. Water is siphoned out of the top of the housing into a vessel. As a result of the siphoned off water, additional water enters the housing via a tube assembly wherein a spray bar assembly rotates and discharges water out of a pair of opposing openings, such discharge causing a vortex. A counterflow vortex is created either by a second counterrotating spray bar assembly or via angled inlet jets on the base proximate the rotating spray bar assembly. The colliding vortexes cause substrate within the aquarium to collide and thereby clean itself. Lighter waste material is carried out of the housing by the laminar water flow of the siphon with the substrate loosing sufficient kinetic energy from the laminar flow so as to gravitationally settle back toward the base of the housing.
