Sponge filters have a limited particulate filtering capacity, but have a lot of surface area for biological filtration. At least every two weeks a sponge filter should be removed from the aquarium and rinsed out with fresh water from the tap (about the same temperature as the tank). A quick rinse with tap water will not likely kill beneficial bacteria, but if you want to be cautious you can use aquarium water.
Cleaning a sponge filter will cause the loss of beneficial bacteria, whether you use tap or aquarium water. Nitrite poisoning can occur a few days after sponge has been cleaned when they are used in an aquarium with limited surface outside the sponge, like bare bottom breeding/rearing tanks. You should test your aquarium water two to three days after a cleaning to make sure ammonia and nitrite stay at 0 ppm.
Because sponge filters have limited particulate filtration capability, aquariums that use them often have detritus collection spots on the bottom that will require removal with a syphon hose or gravel vacuum.
Canister filters are usually placed on the floor, or in the aquarium cabinet. They have two tubes coming out of them, one to draw water out of the aquarium and the other to return clean water back to the aquarium. Canister filters act as a particulate, chemical, and biological filter.
Canister filters have some advantages and disadvantages. Canister filters are often difficult to clean and often do not seal well after cleaning, leading to a leaks.
Marineland's Magnum 350 canister filter can be used as a diatom filter to polish the aquarium water. Diatom power is placed on the outside of the pleated cartridge and helps filter out microscopic particles that make the water yellow. Photo from Marineland.
One advantage of a canister filter is that you can add an ultraviolet sterilizer in line with the return line to the aquarium. Some canister filters use diatomaceous earth (diatom powder) to polish the water. Diatom filters are used only temporarily to remove very fine floating detritus. These filters are usually only run on an aquarium for a couple of hours, before they are removed and cleaned.
If you have problems with a canister filter sealing, you can use petroleum jelly on the “O” ring to get a good seal. This is all it takes most of the time to get a canister filter to seal properly. If petroleum jelly doesn’t work it is probably time to buy a new replacement “O” ring.
Canister filters should be cleaned at least every two weeks. Because canister filters are often hidden away in a cabinet, aquarist often forget to clean them as often as they should (out of sight, out of mind). Canister filters are also more difficult to clean than many other styles of aquarium filters, which also leads to them not being cleaned as often as they should.