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Nitrifying Bacteria
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Within your filter live nitrifying bacteria. The essential microscopic organisms convert lethal ammonia and nitrite into less lethal nitrate. Water flowing through your filter provides these bacteria with the oxygen they need to live. Power off the filter long enough and you stop the flow of water and therefore cut off the bacteria's oxygen supply. When you turn your filter back on, you introduce the dead bacteria into your aquarium, which results in hydrogen sulfide and other toxic substances that can kill your aquarium inhabitants. That means turning off your filter at night is a big no-no. Thomas Giovanetti and Oliver Lucanus, authors of "Discus Fish," suggest unplugging a canister filter for no longer than 30 minutes. You can usually get away with a bit longer -- typically up to another 30 minutes -- for other filters, but there's no reason to leave your filter off that long.
Water Movement
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Some fish enjoy a little current and filter-feeding shrimp require water movement. If you turn your filter off at night, you're preventing filter-feeding shrimp from eating. While the inability to eat at night probably won't kill the shrimp -- they can feast during the day -- the constant stress can cause health problems for the shrimp who can't eat and the fish who enjoy a nice flow of water. Not all shrimp filter feed.
Aeration
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Your fish breathe air mostly from the water, although fish who have a labyrinth organ also breathe air from the surface. When your filter's on, the constant turning over of water pushes oxygen into the water. Higher temperatures, a lack of live plants, some medications and a protein film at the surface can cause reduced oxygen levels, necessitating a need for your filter to push oxygen into the water. Left off all night, you could wake up to some very sick or even dead fish.
Cleaning
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A noisy filter might make you want to turn it off while you're sleeping at night, but there's a better solution, both in the short term and long term. Excessive noise can almost always be attributed to a dirty filter. Turn off your filter and fill a small bucket with enough tank water so that you can submerge your filter. Remove the filter media and disassemble the filter. Every filter is different, so follow the manufacturer's disassembling instructions. Rinse out the filter media and each part of the filter in the tank water -- including and especially the impeller -- and reassemble the filter. Set it back up in your fish tank and turn it on. You should hear significantly less noise. If you don't, you may have a bad impeller, which calls for either replacing the impeller or purchasing a new filter.
If a power outage shuts off your filter for more than 30 minutes, you should also clean it to avoid introducing dead bacteria into your tank.
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Can Fish Live Through the Night With the Filter Being Off?
While it might seem like all your fish tank filter does is turn over your tank's water, it actually plays a vital role in keeping everything healthy and happy. Turn your filter off, even for just one night, and you kill your tank's current, aeration and the hard-working and necessary nitrifying bacteria. If your filter sounds obnoxiously loud and keeps you up at night, a cleaning will usually fix the problem.