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How to Clean a Fish Tank (Beginner’s Guide)

Aquarium maintenance is something that everyone knows to do. But precisely how to clean a fish tank isn’t always obvious.

What are those white, crusty build ups at the water line and why are they so hard to remove? Which brush should I be using on aquarium glass?

This guide breaks down the most common maintenance concerns and walks you through exactly how to clean an aquarium!

Common Cleanliness Issues

Here are a few common issues that may prompt a cleaning:

Foul Water

Whether you’re dealing with green water, cloudy water, overfeeding, or the usual accumulation of nitrate over time, foul water will always be a problem in a contained ecosystem.

Water changes are the best way to deal with general foul water issues. Removing nutrients that contribute to algae and bacterial growth helps bring your aquarium back into balance.

Dirty Substrates

Any guide on how to clean a fish tank will usually show a picture of a siphon hose vacuuming the bottom of the aquarium. Aquarium substrates like gravel and sand tend to allow debris to accumulate over time within.

If you don’t regularly vacuum your substrate, it can become a breeding ground for bacteria and fungi and even become discolored as organisms start to grow within it.

Spots on Exterior of Aquarium Glass

Spotty glass is as common to aquariums as it is to eyeglasses and windows. Whenever water, fingers, or other elements touch glass, they can leave residues behind that mar the aesthetics of your aquarium glass.

Fortunately, cleaning spots from the exterior of aquarium glass is one of the easiest things to do!

Algae and other Biofilms

Biofilm is a catch-all for microorganisms, including algae, that form visible accumulations on glass, gravel, rocks, plants, and even the tubes of filter intakes and other permanently submerged equipment.

Biofilms range from green algae to brown diatom films and even blue-green cyanobacteria. While rarely dangerous, biofilms indicate that some portion of your aquarium’s nutrient cycle is out of balance.

Too much light and free-floating organic nutrients (green algae), too much hard minerals like silica (diatomaceous brown algae), or something else altogether. Fortunately, biofilms are usually easy to clean!

Hard Water Deposits

Of all of the problems here, hard water deposits are one that confound a lot of people. These white, crusty residues form when water evaporates from your aquarium.

If you have relatively hard water, minerals remain from the evaporated water, and accumulate as a chalky crust at the water line.

Hard water deposits are rock-like in texture; when they first form they can sometimes be wiped away with a fingertip or scrub brush. But older deposits will resist all of the elbow grease you throw their way! Mineral deposits require chemical means of control.

Necessary Tools for Aquarium Maintenance

Here are a few tools you may need when cleaning an aquarium:

Siphon Hose

25 Foot - Python No Spill Clean and Fill Aquarium Maintenance System
  • Will not disturb fish or decor during routine...
  • Adapts easily to most faucets.
  • Complete ready-to-use system.

Gravity-powered siphon hoses are a stable of aquarium maintenance.

They come in a variety of sizes and lengths, from 5 feet onto 50 feet or more. They rely on a difference of elevation to function, you’ll need at least 3 feet of height difference to get good flow with a gravity-powered siphon.

If you can’t rely on a height difference or you simply don’t want to carry buckets back and forth, take a look at the Python No-Spill Clean and Fill.

This siphon is powered by water pressure from your faucet, allowing you to vacuum your gravel, perform a water change, and then refill your aquarium without carrying a single bucket!

Water Conditioners

Seachem Prime Fresh and Saltwater Conditioner - Chemical Remover and Detoxifier...
  • POWERFUL TREATMENT: Seachem Prime is a complete...
  • REMOVER: Seachem Prime immediately and permanently...
  • DETOXIFIER: Seachem Prime effectively detoxifies...

Tap water is treated for human use but it’s quite poisonous to aquarium fish. Chlorine and chloramine, added to kill and prevent bacterial growth, cause gill and skin irritation and eventual death in fish.

Chlorine will outgas over time; older aquarium manuals suggest leaving water out for 24 hours.

Many cities use chloramine, however, which was designed to not outgas over time. This makes dechlorinators essential for fish health.

Other water conditioners include pH adjustments; if you have hard water but your aquarium has a soft pH, you’ll want a solution to lower the pH closer to your aquarium’s current level.

Likewise if you need to raise the pH of your added water. Water chemistry test strips ensure your parameters are optimal; drastic changes can be fatal to fish!

After adding chemical adjustments, stir the water by hand for good mixing and wait 5-10 minutes before retesting or adding to your aquarium.


Newspaper is one of the best materials for cleaning the outside glass. The consistency of its fibers and its absorbent nature leaves a streak-free exterior with simple distilled water without resorting to chemical-laden sprays that can be poisonous to fish.

If you don’t care to keep newspaper around, microfiber cloths are another great way to reduce streaking as you clean the exterior of your aquarium.

Magnetic Scrubbers, Sponges, and other Cleaning Pads

It’s always good to keep a few different types of cleaning pads near or under your aquarium. Most are made of various synthetic materials that are tough yet won’t scratch your aquarium.

Knowing what type of aquarium you have is quite important; glass aquariums are more resistant to scrubbing while acrylic aquariums can be scratched far easier. Many pet stores carry brushes and pads made specifically for acrylic tanks, like API’s Algae Pad.

I also keep steel wool but I highly recommend that you use it as more of a tactical nuclear option. Steel wool doesn’t usually scratch aquarium glass but depending on the grade, can cause faint scratching with heavy use. It will absolutely scratch acrylic aquariums, however.

Steel wool is a great tool for a stubborn spot or a hidden corner but I don’t recommend using it over the entire front glass panel, for instance. Steel wool also has a tendency to fall apart with repeated use, leaving metal bits within the fish tank that can cause problems.

Magnetic scrubbers are popular for cleaning the inside glass without getting your arm wet. Personally, I’m not a fan because they don’t create as much pressure as cleaning by hand. Also, you’ll eventually misalign the magnets, causing the inner one to drop off. Which you’ll need to then fix by reaching into the aquarium. But for a quick scrub of soft biofilms on one panel of glass at a time, they are useful.

White Vinegar

This last one is a bit strange but is the perfect tool for dealing with hard water stains. The acidity of white vinegar reacts with the hard water stains, making them softer and easier to remove!

How to Clean a Fish Tank

Ready to take the plunge into cleaning your aquarium? Here are our recommendations for a sparkling clean tank.

Changing Your Aquarium Water

Water changes should be done weekly or bi-weekly but a lot of this depends on your setup. The more frequently you do water changes, the smaller they should be, with 10% a week a good average. The number and size of your fish, substrate type, plants, what type of filtration you use, and how heavily you feed all plays an important role. But to summarize: the less biological filtration you have going on (i.e. microorganisms and plants) the more you should be stepping in to change the water and keep things tidy.

Water changes can be done either with a siphon hose or a cup or bucket. Draw off aquarium water, dispose of it (house plants love it!), and add water of the same temperature and chemistry (see earlier section on Water Conditioners).

When pouring water into the aquarium, don’t simply dumb the entire amount in. Gravel and plants can be disturbed, fish can get caught under the flow and hurt, and splashes can happen. Pour gently and evenly until your container is empty

Vacuuming the Substrate

When vacuuming the substrate with a siphon hose, I recommend going straight for the gravel. Plunge the open mouth of the siphon down into the gravel, all the way to the bottom of the tank, and then lift the end so gravel starts to run back out. The lighter feces, old food, dead plants, and other material will follow the water flow up into the siphon hose.

Large gravel has a tendency to get impacted within the siphon hose, especially if your gravel bed is deeper than 3 inches. A gentle shake of the siphon hose or soft taps against a hard surface will dislodge the gravel. Be careful not to let gravel fill up the siphon hose head or it will get swept up in the flow and get carried out of the fish tank.

Once the flow of debris slows or stops entirely, follow the above directions on changing your aquarium water.

Cleaning the Front Aquarium Glass

While Windex and towels are what people often go for, there are cheaper ways of cleaning the front glass that are also better for both you and your fish’s health. Newspaper and vinegar is a popular combination that does the job just as well.

First, check to see if your local newspaper uses a petroleum-based ink or a soy-based one. Many papers have an official Soy Ink Seal to showcase their commitment to an environmentally sustainable cause. Over 90% of US newspapers currently use soy ink; a good test is to grasp the paper between thumb and forefinger for a minute. Petroleum-based inks will stain your fingers and isn’t good for glass cleaning.

Don’t use chemical sprays on your aquarium glass. Really, you shouldn’t be using them anywhere; they’re bad for you as well. A 50/50 mixture of white vinegar and water is perfect for disinfecting and cleaning the front glass (as well as your bathroom mirror). Combined with your petroleum-free newspaper, you’ll have streak-free glass in no time!

Cleaning Algae and other Biofilms Within the Aquarium

Biofilms are a constant part of aquarium life; so long as you have living creatures, you will see microorganism growth of one kind or another. Truly, you should be more worried if there are no biofilms present. What we want is to keep them in control, not to eliminate them.

Most biofilms are easily removed with an aquarium scrub brush. Stubborn biofilms that grow flush with the glass, may require a razor blade to remove. Remember that glass and acrylic have different cleaning requirements; acrylic is lighter than glass but also less scratch resistant. Special acrylic pads are needed for tank maintenance.

Common places for biofilm accumulation include the substrate, rough surfaces like rocks, flat surfaces like plants and glass, and tank equipment like filter in and out takes. If you use plastic plants, removing them and scrubbing them in a sink or bucket is the best way to get them looking new again. Stubborn biofilms can also be killed by letting decorations dry in the sun for a few days before brushing them and returning them to the aquarium.

Brown bacterial mats sometimes form on the outflow of hang on back filters. While harmless, they are often unsightly. Fortunately, these growths are quite soft and wipe off easily with a sponge or brush.

Biofilms on substrate are a bit more challenging to clean. Blue-green cyanobacteria usually comes off with a gentle siphoning as it normally forms a coating directly on the surface. But if you have stubborn green or brown algae, you may need to take more drastic measures.

Spot treatments of hydrogen peroxide from an eyedropper can help kill off persistent growths but beware; H2O2 is slightly toxic to all organisms. Turning over the gravel will also deny green algae light and lead to death. Any sort of treatment, chemical or physical, should work alongside your efforts to address the root cause of the overgrowth, which is always light or nutrient imbalance.

Removing Hard Water Deposits

Hard water deposits are a sign that you have medium to high levels of minerals in your water. Unless your fish require soft, acific water, this isn’t really a problem except for maintenance issues.

When hard water stains first begin to form, a bit of elbow grease or a sharp razor blade can remove them from the water line. But as you refill your aquarium again and again, the deposits form regions with increased surface area relative to the flush glass. Minerals will accumulate here, forming hard crusts impossible to remove by hand.

White vinegar is once again our friend. As an acid, vinegar will break down and make hard water stains easier to remove. You’ll want to use store-bought white vinegar, dabbed on with a sponge to minimize the amount that enters your aquarium. Being acidic, vinegar will cause drastic shifts to pH that can cause harm to organisms, especially in small aquariums.

Give the vinegar 5-10 minutes to penetrate, and then test removing it with a scrub brush or razor blade. Dab on more as needed until the crush eventually comes off. The best medicine is prevention with mineral deposits; the longer you let them go, the harder they are to remove.


Knowing how to clean a fish tank need not be a hassle.

There are many methods of accomplishing each of these tasks and you’ll eventually find tricks that work best for your maintenance schedule.

What’s key is to keep your cleanings light and regular; that way you rarely have to do heavy, disruptive cleanings!

Jason Roberts
About Jason Roberts
Jason is an aquarium fanatic that has been a fish hobbyist for almost three decades.

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