How To Clean a Fish Tank

Learning how to clean fish tank correctly is a major part to keeping your pet fish happy and healthy. Here are some key points to consider when cleaning a fish tank.

How To Properly Clean a Fish Tank

All aquarium cleaning equipment should be used only to clean your fish tank. Clean you fish tank using these steps:

  1. Wash your hands thoroughly before putting them in contact with fish tank water

  2. Turn off your filtration, heater, and lighting.

  3. Remove decorations from your fish tank and place in separate bucket or on a towel. Scrub your décor using a designated scrub brush and/or toothbrush.

  4. Scrub sides of fish tank using acrylic or glass scrub brush.

  5. Place siphon into your fish tank and start the flow into a bucket. Move the siphon up and down, taking in a small amount of substrate at each site. Allow it to circulate for a second or two, then lift the vacuum to break the siphon.

  6. Move the siphon over slightly and repeat across the entire bottom of your tank.

  7. Remove your tank’s filter media (sponges, balls, floss, or rocks) and rinse them in the bucket of waste water. Note: Never replace your filter media unless it is falling apart.

  8. Rinse and fill your bucket with fresh tap water. Use your thermometer to ensure it is the correct temperature for your pet fish.

  9. Add your water conditioner per the manufacturer’s instructions. Only add enough to treat the water in the bucket.

  10. For salt systems, add the correct amount of salt to your bucket and allow it to circulate for five minutes.

  11. Add fresh water slowly back to main tank.

  12. Return your décor back to the tank.

  13. Once refilled, turn on your lights, heater, and filtration. Filtration may need to be primed for correct operation. Refer to manufacturer’s instructions.

  14. Wash your hands!

How Often Should You Clean a Fish Tank?

Fish tanks must be cleaned on a routine basis. Regular cleaning keeps your pet fish healthy by removing waste and providing clean water to breathe. Cleaning is essential in the early stages of a fish tank setup to complete your fish tank’s nitrogen cycle. Once established, your tank will still require regular cleaning.

Your tank cleaning maintenance schedule will depend on the size of your fish tank, the total number of pet fish, and your filtration setup. The best way to know if your fish tank cleaning schedule is adequate is to test your water chemistry. If any of the following parameters are out of range, you will need to perform some maintenance. Basic recommendations for fish tank cleanings are at least 10% weekly to 25% every other week for established tanks.

If any of your water quality parameters are above these limits, it’s time for a water change. Levels are based on standard API test kit ranges:

  • Ammonia > 0.25 mg/L

  • Nitrite > 0 mg/L

  • Nitrate > 20 mg/L

Never remove more than 50% of the total water from your tank at once. This will prevent sudden changes in pH and temperature from stressing out your pet fish. Always use a water conditioner if you are using tap water to ensure no exposure to toxic chlorine. If you are concerned about your water chemistry, contact your fish veterinarian.

Ignoring or performing inadequate cleanings can result in increased health issues and even death in your pet fish. Buildup of debris, excess food and waste can result in increased ammonia levels which are toxic to fish.

Do You Take Fish Out of Tanks When Cleaning?

Do not remove your fish during cleanings. This will cause unnecessary stress. Provided you are cleaning a fish tank properly, your fish will not be in the way during cleaning.

The only reason you would need to remove your pet fish is if your substrate is less than 3 inches deep and smells like rotting eggs when disturbed. This indicates the presence of hydrogen sulfide which is toxic to pet fish. In this case, you will need to remove the gravel and replace all the water. Move your pet fish into a holding tank with their filtration, this will give them adequate space to hang out while you do a deep clean of the fish tank.

How To Safely Clean Your Fish Tank

During the cleaning process, your pet fish should not swim up the gravel siphon. If they try to, quickly lift the siphon above the water line, causing the water to pour back into the tank.

Always turn off all electronic components when cleaning. You can still run an airstone if you are concerned about fluctuating levels due to a high plant or algae load or your fish have intermitted periods of lethargy or are recovering from a gill-related disease. If your system has a sump, it may start to back siphon and overflow your sump. Be sure to break the siphon or turn off access to the sump during cleaning to ensure things don’t get too wet.

As with any pet, there is a risk of communicable diseases. Fortunately, with pet fish, there few diseases of concern. Zoonotic (spreadable to humans) mycobacterial infections are the biggest issue which can cause non-healing lesions on skin. If you have any open cuts or sores, do not expose yourself to tank water.

Do not allow children or anyone with compromised immune systems to handle waste tank water or any components.

Freshwater Fish Tank vs Marine Fish Tank Cleaning

When it comes to comparing cleaning freshwater and marine aquariums, there is no difference in the fish tank cleaning process. The concern is around live coral fish in the saltwater tanks. Obviously, these pet fish cannot be removed for cleaning and must remain in the tank. You may need to shift them slightly to vacuum underneath them.

What You Need To Clean a Fish Tank

Water Quality Test Kit: Testing your tank’s water chemistry will tell you when it’s time to do a water change. Refer to the parameters above and be sure to test your water chemistry at least once a week.

Tap Water Conditioner: Unless you are using bottled spring water or reverse osmosis water, you will need to treat all tap water for chlorine and chloramine. Reverse osmosis (RO) water is made by passing tap water through a very fine filter, removing almost all particulates, including small ions contributing to your water’s total hardness and alkalinity. Depending on your RO filter, you may have additional removal of chlorine and chloramine. Chlorine products are added to municipal water systems to ensure it is safe for humans to drink, but toxic to pet fish.

Gravel Siphon: No matter what substrate you have in your tank, it can easily build up with waste. Proper vacuuming is an essential part of your maintenance routine. Just stirring up the substrate will not keep your fish tank clean. These vacuums do take a little practice, so just be patient and understand there will be a learning curve until you can use it easily.

If you want the best gravel siphon available­–check out the Python System.

Algae Scrubber: Algae in your fish tank is actually a sign that your tank is healthy! If you need to clean the walls of your aquarium, pay special attention to the material. Glass aquariums can use more abrasive scrub brushes than acrylic tanks and can scratch acrylic tank walls. If you are unsure of which material you have, stick to the safer acrylic sponge.

Thermometer: When adding new water back into your fish tank, make sure it is the same temperature as the current environment to avoid stressing out your fish. Infrared thermometers will take an instant reading and allow you to change your water temp prior to adding it to your system.

Refractometer: For saltwater systems, there are many to choose from, but ensure that everything is mixed correctly before adding it to your system. A quick check with a refractometer is essential to ensure your system’s salinity stays within range.

Featured Image: M-Production/iStock / Getty Images Plus via Getty Images


Hashish E, Merwad A, Elgaml S, et al. Mycobacterium marinum infection in fish and man: epidemiology, pathophysiology and management; a review. Vet Q. 2018;38(1):35-46.


Jessie Sanders, DVM, DABVP (Fish Practice)


Jessie Sanders, DVM, DABVP (Fish Practice)


From the love of animals and the underwater world came the most unique and amazing veterinarians on Earth, Dr. Jessie Sanders. Dr. Sanders,...

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