Cleaning your Freshwater Aquarium

by Susan Horton, DVM

Why should you clean your aquarium? No matter what type of filtration you have, you will need to regularly clean your aquarium. In a balanced, stable aquarium uneaten food or fish waste turns into ammonia. “Good” bacteria then convert these pollutants into non-toxic “nitrates”. Without regular water changes, the “good” bacteria will not be able to keep up with the accumulation of uneaten food or fish waste and the ammonia will quickly reach a dangerous level. How often should you clean your aquarium? There are many different opinions as to how often a tank needs to be cleaned. In general, the more often you clean your aquarium, the healthier your fish will be. In new aquariums (less than 3 months) we recommend a 1/3 to ½ water change every two weeks. As the aquarium becomes older a water change once a month should be sufficient. We do not recommend you take more than ½ of the water out at any one time. How should I clean my aquarium?

  1. Before starting, always take a minute to monitor your fish. Look for any signs of illness or stress. Clamped fins, loss of color, lethargy or tiny white dots (ICH) are all signs of stress. If you see any of these symptoms, proceed with your water change and consult your pet store about water testing.
  2. Unplug all equipment and wait ten minutes for your heater to cool down before starting to siphon any water out.
  3. During this time you can clean any algae off the glass so it will be siphoned out. Always use aquarium-approved products when scraping algae. Many other products will scratch the glass or could introduce harmful chemicals into the tank.
  4. Always use a “gravel cleaner” when siphoning water out of the tank. Never siphon water off the surface of the aquarium because waste accumulates at the bottom of the aquarium. By using a gravel siphon, you will be able to lift up gravel and get rid of the waste without removing any of the gravel or the fish. If you need to see a demonstration of how to use a gravel-cleaner, stop into your pet store and ask for a demonstration.
  5. Siphon the water into a bucket that is only used for the aquarium to prevent any type of accidental contamination.
  6. Before dumping the water out, clean the foam part of your filter in the dirty water. This way you will not harm the beneficial bacteria growing on the sponge. Replace any of the other cartridges that need to be cleansed (carbon should be replaced one a month). If you need to replace both the carbon and the foam we recommend you do this three to seven days apart so your filter will keep some of the established bacteria.
  7. Refill the tank one bucket at a time with tap water. Try to get the temperature close to the aquarium temperature. Add any water conditioners necessary into the bucket. Gently pour the water into the aquarium. Repeat, until the tank is filled. Wait five minutes and plug your equipment back in.


  • Never use soap or any household cleaners on the inside or outside of your tank.
  • If your filter doesn’t start back up, make sure the impeller is clean of grime.
  • Never change more than 50% of the water at any one time.
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