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What Does It Mean to Clean an Aquarium? A Guide for Beginners.

April 01, 2019 3 min read

If you've ever emptied your tank, removed all the substrate and rocks, and scrubbed everything down in the sink before putting it all back to normal, you probably caused more harm than good. Not only is this traumatizing for your fish, but it could be deadly for the essential bacteria living in the substrate and crevices inside rocks. These bacteria cannot survive exposure to chlorine, which we know is deliberately added to tap water to kill bacteria. With the filter media as the only other home for your bacterial companions, this exercise in "cleaning" destroys half of your biofilter in an instant, which could take weeks or months to revive. In these conditions, replacing your animals could potentially be hazardous, as the reduced capacity of the biofilter could lead to a build-up of poisonous ammonia.

Follow this general cleaning guide for a healthy aquarium. In most cases, you'll want to avoid removing anything for cleaning. And remember chlorine kills bacteria, so make sure tap water never touches your aquarium or anything inside it without first being treated with a dechlorinator. If you decide to remove something for cleaning, use a bucket of tank water from a recent water change. 

Over time, the filter sponges and other filter media will get clogged with debris. Not only will this reduce the filtration capacity of your system, but also the debris will build up and increasingly release acids into the water. As a general guide, you should clean your filter monthly, but of course this can vary depending on a number of factors. Remove the filter media and massage it in a bucket of old tank water from a recent water change (don't rinse it in tap water). Also, its good practice to clean only one filter chamber at a time, alternating each month, in order to reduce disruptions to the biofilter.

The single best cleaning exercise you can do is a weekly 25% water change. This will remove nitrates and other waste products that would otherwise build up, acidifying the water and promoting algae growth. Plus, new water is needed to replenish essential minerals that are constantly being depleted. The percentage of water that you replace can of course be adjusted based on your testing results, which you should also be gathering weekly. See our testing guides for reef or planted aquaria.

If the aquarium walls are grimy, simply wipe them down with a razor blade or algae eraser. Never use soap, Windex, or any other cleaning agent.

It's best to avoid removing the substrate to minimize disturbance to bacterial colonies, burrowing animals, or delicate plant roots. When cleaning is required, the process depends on the type (sand, gravel, aqua soil). For gravel, a gravel-vac is usually the preferred tool. Sand might get sucked up by a gravel vac, so "blasting" is a more functional method: Use a turkey baster or similar tool to lightly "blast" the sand bed, kicking up debris, and then immediately pass a siphon tube over, at the correct distance to catch the debris but not the substrate. This is sensible to do when removing water for a water change, and will also help to aerate the substrate layer. Aqua soil is best left undisturbed, so organic debris can settle, decompose, and turn into plant nutrients. If necessary, lightly blasting an aqua soil layer can help clean it without causing too much of a disturbance. If you must remove the substrate for cleaning, do so in batches, and do not rinse with tap water.

Rocks, Wood, Hardscape
The crevices in rocks and wood house essential bacteria, so it's best to avoid removing these objects. If you must remove them for cleaning, do not rinse with tap water.

-By Aqua Lab Aquarium Team

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