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Cleaning Your Freshwater Fish Tank

Updated on November 19, 2014

What Needs to be Cleaned

When cleaning a freshwater fish tank, it is not only important to know how to clean it but what you should and shouldn’t clean. If you happen to have live plants, driftwood, or any number of bacteria habitats you wouldn’t want to clean them for fear of killing off the bacteria and sending your tank into a state of shock. Without the bacteria, ammonia, nitrite and nitrate levels could grow exponentially and kill your fish. Cleaning artificial plants and ornaments is fine as long as you are sure they are not the main bacterial habitat (they usually aren’t unless they have set up shop on the exposed underside of an ornament.

Of course the major reason most people clean their fish tanks is to remove algae from the glass. Although having fish to do this is the optimal choice there are several tools that can be used to achieve cleaner aquarium glass.

The filter system needs to be cleaned out periodically as well. Over the side filters should have their cartridges changed out every three months and the components cleaned at the same time.

How to Clean Aquarium Glass

One of the first things that you need to learn when learning how to clean a fish tank is cleaning the glass. The outside of the glass can be wiped down with Windex or any other glass cleaner as long as you spray it on a rag first and not directly on the tank glass. Stray glass cleaner contains several poisons that will kill your fish. Never spray the glass cleaner over an open tank, in fact it is best to spray the rag in the opposite direction of the tank.

The interior of the tank is another matter altogether. There are several products available to help clean the inside glass of the aquarium including scrapers, power scrubbers, magnets and various sponges. Although many of the more expensive gadgets, including the battery powered scrubbers, look like they will do the job they actually aren’t as reliable as a cello sponge and some elbow grease. Plastic scrapers work well on tough brown algae and calcium deposits, I use a small kitchen scraper for this. Many aquarists use magnets lined with felt to make easy work of algae. One magnet is placed inside the tank and the other on the outside. Dragging the magnet across the glass effectively scrubs the algae off. It is important to be careful with these magnets because a single stray piece of gravel that gets under the felt and in between the magnets can cause scratching on the inside of the aquarium. Getting these scratches out of a glass aquarium is not easy.

The easiest way to clean the interior glass of your fish tank is to purchase a small sponge on a stick. A lot of these come with scrapers on the front (they look like miniature windshield scrapers). They will allow you to reach to the bottom of your tank without having to submerge your whole are. The leverage they give will allow you to remove even the toughest algae without straining yourself. This is definitely the best way how to clean your fish tank glass.

How to Clean Aquarium Filter Systems

If you are wondering how to clean a fish tank filter first you have to realize that there are three major types of filtration systems that are used in freshwater aquariums; under gravel filters, hanging filters and canister filters. Under gravel filters are the hardest to clean although they need to be cleaned the least often. To clean an under gravel filter you need an aquarium vacuum. These can either be powered or gravity driven. A gravity driven vacuum requires you to get the water flowing by suction (this can leave a bad taste in some people’s mouths). If you use the vacuum once a week it will prevent serious build up that can result in toxic situations for your fish. Many bacterial colonies can inhabit the under gravel filter so cleaning with the vacuum could eradicate them. If you are using an under gravel filter you should have a secondary area for your bacterial colonies. Cleaning an under gravel filter thoroughly requires removing it from the tank – this is usually only done when there has been a catastrophic event that has killed off most or all of the fish in the tank.

Hanging filters (or Hang on backs - HOB) are much easier to clean thoroughly. Once every couple of weeks you should remove the filter cartridge and rinse it off in cold water. Use water from an outside hose if possible as tap water contains several potentially hazardous components. If you can’t use an outdoor source use bottle water. If this is not an option after rinsing the filter in the sink soak it in a bucket with a chemical remover like Prime to remove any chlorine or hard minerals that may be present. Changing the filter cartridge every three months is a must as the filter media will clog otherwise, even with the periodic rinsing. When you change the cartridge you should also wipe down the intake column. The plastic intake pipe is one of the only places that algae eaters cannot do their job. The interior of the column will probably be full of algae. Clean this out with a sponge. If the tube is too long to reach into you can rip a small piece of sponge and force it down the inside of the tube. Use a pencil to push it out the other side. This will remove the algae growth and give a crystal clear look to the intake. If the rest of the filter is beginning to look dirty you can wipe it down in the bathtub or kitchen sink at this time as well.

Canister filters are far easier. You can remove the entire unit from the tank and take it to a utility room before emptying it. There will be a lot of muck around the foam insert that protects the motor housing. This will rinse away quite easily. The interior of the canister should not be rinsed out! This is where the biological filter media is stored and where the bacterial colonies live. If you clean it you’ll kill off the bacteria. Wipe down the outside of the canister and the protective foam block only.

How to Clean a Fish Tank’s Plants and Ornaments

The ornaments and plants in a fish tank sometimes need to be cleaned as well. If there is a build up of algae on ornaments they can be cleaned with the sponge on your glass cleaner or you could remove them from the tank and wipe them down with a mixture of 1 part rubbing alcohol to 3 parts water. This will kill off the algae and any possible pathogens on the ornament. Do not use bleach. Even a little left over bleach entering the tank can kill of bacteria, plants and depending on the amount, fish. Plastic plants can be handled the same way. Some people even run ornaments and plants through their dishwasher. This works well with sturdy, well made ornaments but the flimsy ones tend to warp due to the hot water. If you do use the dishwasher don’t use soap, the residue could be harmful to your fish.

Live plants are an entirely different story. Cleaning live plants requires the utmost care. Remove the plants from the tank and set them on a damp paper towel. Algae growth on the plants can be removed by wiping it away with a paper towel. Gently rub the algae off the leaves of the plant making sure not to damage it in any way. Again, this is very delicate work and some of your plants will get damaged. Remove the damaged leaves before returning the plant to the tank.


Once you’ve learned how to clean a fish tank it is easy to maintain it. Remember, the longer the time between cleanings the harder the cleaning will be. Small maintenance cleanings can be done once a week to make the yearly big clean much easier.

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