A system for filtering and treating waste generated or collected in the water of a fish pond. The system includes a pump, pre-filter, piping, a valve assembly, and a filter media container enclosing a plurality of discrete filter media. The filter media are generally hollow, plastic structures with a plurality of external ribs and internal dividing walls. The filter media has a high surface area-to-volume ratio and can support a high volumetric density of naturally occurring heterotrophic bacteria. The heterotrophic bacteria establish colonies on the internal and external surfaces of the filter media and biologically metabolize waste that is trapped on the media. The bacterial metabolization transforms much of the waste to an aesthetically and biologically neutral form thereby reducing the need for chemical treatment of the pond water. The system includes a backwashing mode to agitate and remove unreacted waste from the system and direct the waste stream out of the system, preferably to be used as fertilizer.