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How to Clean a Dirty Fish Tank

dirty aquarium

Although regular maintenance should prevent your aquarium from getting to a point of being “dirty”, sometimes additional food or the addition of a few new finny friends may cause some additional waste and extra care may be needed in getting an aquarium back to where it is needed as a safe home for aquatic life. If possible, draining the aquarium completely should be avoided as beneficial bacteria is necessary to create a healthy ecosystem and the nitrogen cycle will need to start over completely if everything is taken out. The steps below will discuss the best way to get your aquarium back on track without completely starting over as well as how to maintain a clean aquarium.


  1. Siphon/gravel vacuum
  2. Bucket (specifically for aquarium use)
  3. Water dechlorinator
  4. Algae scrubber/scraper
  5. Glass cleaner
  6. Towels
  7. Bleach

In Preparing your work area

Before performing any maintenance on an aquarium, hands should be thoroughly washed and rinsed to prevent introducing any lotions, perfumes, or other toxic chemicals to the aquarium. Gloves may also be worn to protect hands as well as the aquarium water. All supplies such as sponges, siphon, and buckets should be designated for aquarium use only to remove the risk of accidentally exposing your aquarium or accessories to harmful chemicals. Once supplies are all gathered, cleaning can begin!

Cleaning the glass or acrylic walls of your aquarium

Algae and any buildup will need to be removed from the walls inside your aquarium. An Aquarium Glass Scrubber & Scraper is a useful tool that aids in removing even stubborn algae and debris from the glass. The sponge-like scrubber area can be used to remove most build-up with ease while the scraper may be needed for more stubborn algae or when it has grown in hard-to-reach places such as corners and edges of the aquarium. If your aquarium is made of acrylic instead of glass, be sure to use specialized scrubbers for acrylic to reduce the risk of scratches to your aquarium, as this material is more sensitive than glass and can be easily scratched. Regularly wiping down the walls of your aquarium during routine maintenance will help reduce buildup of mineral deposits or algae that require more elbow grease to remove.

Cleaning décor and accessories

Any decorations including artificial plants, rocks and accessories can also collect waste and algae in the aquarium making it not only unsightly, but a buildup of debris is also adding to an unhealthy living environment for your aquatic life. Removing the décor from the aquarium and scrubbing under hot water with an algae pad will loosen most debris from these items, but in some cases a more thorough disinfection may be needed. A diluted mixture of water to 3 % bleach may be used to remove stubborn build-up or disinfect if needed. Accessories should soak in the solution for 15 minutes before being thoroughly rinsed, scrubbed, and allowed to air dry. If any smell of bleach remains once dry, you will need to soak in a bucket containing dechlorinator to ensure no residual bleach is introduced to the aquarium.

Cleaning the Filter

Depending on the type of aquarium filter you have, the maintenance level and specifics may vary. During routine maintenance your filter should be inspected to verify all parts are working properly and any buildup of algae or debris is removed. Removing your filter from the aquarium and placing it in a bucket of dechlorinated or aquarium water can be the easiest way to remove excess waste without removing all beneficial bacteria and disrupting the balance of your aquarium. Be careful to not use hot water, bleach or chemicals as this will kill beneficial bacteria that should ideally be preserved. Use the dechlorinated or aquarium water and an algae pad to scrub any areas that need build-up removed on the non-media parts of the filter.

Biological filtration media should not be replaced nor rinsed and disturbed as little as possible as to not destroy beneficial bacteria that inhabits it. Other types of filter media, such as sponge filters, filter pads or carbon, may need to be rinsed or replaced depending on the type being used. Chemical filtration media, like carbon, should be replaced every 3 to 4 weeks. Once everything has been cleaned and replaced, the filter can be placed back on or into the aquarium.

Water Changes and Gravel Vacuuming

While décor and accessories are drying, excess debris will need to be vacuumed during a water change to remove excess waste that contributes to toxic ammonia and the accumulation of nitrates in the water. Removing and replacing no more than 25% of the water is recommended for routine water changes to prevent disrupting the beneficial bacteria. In unusual circumstances where a significant amount of water is being removed, filters and heaters may need to be unplugged to prevent burn-out while running without sufficient water levels. A siphon vacuum can be used to remove waste from the aquarium substrate and efficiently drain water for a water change.

To prepare for an efficient water chance and remove the most debris, start by taking your algae pad or hand and scrubbing through the gravel to loosen any algae and waste. Once you have thoroughly scrubbed and stirred the gravel, allow a few minutes for the debris to settle to the bottom of the aquarium. After everything has settled, using a siphon in a slow up-down motion, move around the aquarium in a strategic manner to vacuum up the debris from the bottom of the aquarium. Remember, try to remove excess waste without over disturbing the substrate and still leaving as close to 75% of the aquarium water as possible to maintain proper beneficial bacteria levels. Read How to Use a Gravel Vacuum for more details on vacuuming your fish tank.

Adding clean décor back into the aquarium.

Once the gravel has been vacuumed and décor and accessories have been verified to not retain any smell of bleach, they may be placed back into your aquarium. New water, that has been pretreated with water conditioner to remove harmful chlorine and chloramine and detoxify heavy metals, can be added into the aquarium to replace the dirty water that was removed. Once an optimal water level has returned, filters and heaters can be plugged back in and restarted if necessary.

Cleaning the outside of the aquarium

Once everything has been placed back into your aquarium, there may be some spills and water spots that need cleaning up. Using a glass cleaner specifically developed for aquariums is vital to reduce the risk of accidently adding toxic chemicals found in regular glass cleaners to your aquarium. This cleaner can be sprayed on a towel and the outside glass wiped down to remove any water spots, mineral deposits, or fingerprints from the outside glass for a clear and pristine view into your aquarium. If you have an acrylic aquarium, it is important that you utilize a produce made for acrylic. Many household glass cleaners can break down the acrylic making it look cloudy. Use a towel to clean up any spilled water around your aquarium or on the floor. Your aquarium is now ready for ultimate viewing and your aquatic life will be happy with their newly cleaned home!

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Reviewed by Don Spaeth, Petco’s National Aquatic Care, Education and Programs Manager

Don is Petco’s National Aquatic Care, Education and Programs Manager. He is an avid aquarist who has worked with and cared for freshwater and marine aquatic life for over 40 years. Throughout his 27+ years with Petco, Don has actively been involved with our aquatic vendor partners and worked to promote aquatic education both in store and company-wide.