The filter plate, and substrate provide the media on which nitrifying bacteria can colonize. Undergravel filters tend to do a good job at maintaining healthy biological cycles in freshwater aquariums. Their main drawback is the effort required in cleaning them. This means that one must completely pull up the filter plate during cleaning, which is a real chore. Still, they have proven to be very efficient and reliable.
Box filters are the other main filtering system one finds in freshwater aquarium setups.
They consist of a small pump, filter, and carbon insert, all housed in a box which sits on the back of the aquarium. Water is drawn in through a small tube which extends into the aquarium, and flows back into the tank by passing through the filter on to an overhanging lip. These filters provide biological, mechanical, and chemical filtration to the aquarium. The filter acts as the media for colonizing nitrifying bacteria, which provide the biological filtration. It also traps debris in the water, which is the mechanical filtration.