How to Clean a Fish Tank

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Fish tanks are great, but learning how to clean them has a bit of a curve. It’s just one of those bits of tank maintenance that no one seems to talk about, which can make many people nervous. It’s not nearly as hard as it looks, it’s mostly just a matter of learning when to do what.

Let’s get right to it, and we’ll discuss how to clean a fish tank and what you need to do it.

cleaning a fish tank


What You Need

There are a few different things you’ll need to get together before you get to cleaning. You can’t use any of the normal supplies that you’d use to clean glass, since the vast majority of cleaning chemicals are highly toxic to fish.

  • Gravel Vacuum A gravel vacuum is a simple siphon that will help you pull detritus from the floor of the tank. Very small tanks may need a smaller vacuum than the one linked.
  • Algae Scraper For manually removing algae, you’ll want an algae scraper. You can also use a razor blade in smaller tanks, but it can be much more difficult to scrape the entire surface of the tank. Even with maintenance, a scraper is useful for removing hard water stains.
  • Magnetic CleanerFor continued tank maintenance. Preventing the regular formation of algae will make your job much easier in the end.
  • Aquarium Test Kit Most dirty tanks also have dirty water. You need to know how dirty and if there are any dangerous contaminants in the water to proceed.
  • A Bucket- We’ll fill it with tank water to clean equipment. Five gallons is enough for most purposes.

You may also want a pair of gloves, depending on how comfortable you are having your hands in water. Elbow-length rubber gloves, like those used for cleaning dishes, will do the trick in most cases.

I also recommend keeping a separate maintenance log for each tank. This will let you know how well long-term efforts are going since you’ll know when you last performed any cleaning or maintenance tasks.

1. Clear the View

We want to clear the glass of the tank before we even begin pulling water. An algae scraper is ideal for handling this. In minor cases, a magnetic cleaner can do most of the heavy lifting.

Be as thorough as possible, you want to get any algae or caught detritus on the glass off of it. It’ll fall to the bottom of the tank, creating a mess if there’s a serious algae problem, but we’ll be picking all of that up in just a bit here.

It’s not advisable to use chemicals, even white vinegar, to remove hard water stains from the top of the tank. The minor build-up will come off easily, but if it’s been a while since the last time you did maintenance you may be in for a chore.

Calcium stains scrape off much more easily underwater, but if the tank has evaporated a bit you can just keep the razor blade or tip of the algae scraper wet. I find a razor blade is more handy if you have a normal level of build-up, but it can be exhausting on larger tanks.

The best way to avoid hard water stains? Keep the tank topped off with distilled water to keep all of the available calcium salts dissolved.

Once you’ve cleared the glass, it’s time to grab the test kit to determine how much water to remove.

You may need to move equipment around at this point, in which case you should place it in the bucket. Do not fill the bucket with tap water.

2. Test the Water

Test water for ammonia, nitrite, and nitrates. In a cycled tank there will be no presence of the first two, most of the time we’re just going to be dealing with excess nitrates.

If your readings are over the desired level for your tank, then you’ll need to do a sizable water change and may need to up the schedule on changes in the future. Algae blooms are one o the unfortunate side effects of high nitrate, making it a good idea to control them when possible.

Anything over 20ppm of nitrate should be acted upon. 

Any nitrite or ammonia in the water means there’s a problem in the nitrogen cycle that should be addressed. That means stalling the addition of any other fauna and gauging the danger your fish are in. Very hardy fish may be able to handle small amounts, but other fish may need to be relocated to a cycled tank immediately.

If nitrates are very high don’t attempt to reduce it all in one go. Just start making water changes at an increased rate.

3. Spot Check Plants and Decorations

You can knock brown or green algae free from most decorations with just your hand. Don’t fret over green spot algae on slow-growing plants like the various Anubias sp. That stuff isn’t coming off regardless of what you attempt to do.

In the meantime, any real plants in the tank should be maintained. Cut off leaves with holes or rotting stems and rub off any brown algae you see on the plants. Don’t worry about where it goes, it’ll come up when we vacuum the bottom.

Do the same with rocks and driftwood. Your goal is just to get as much of the stuff off as possible, preventing further build-up even if removing all of the material is almost impossible.

Do any normal plant maintenance at this time as well. For once you can just grab any loose cuttings with the net and not worry about most of it, since you’ll be cleaning up anyways.

There’s one exception to the algae rule: if you’ve got a significant presence of blue-green algae then move your fish into another safe tank before disturbing it. They can release toxic gasses that are surprisingly deadly into the water column.

In fact, if you have a significant (ie: visible) presence of cyanobacteria at all you have a major problem. You can fix circulation and nutrient issues for the most part, but in my experience… cyanobacteria will keep coming back until you actually sterilize the tank, substrate, and hardscape.

4. Vacuum the Bottom

You’ll now use the gravel vacuum to begin siphoning water out of the tank.

Dig around in the substrate a bit, you’ll be surprised at how much detritus can end up being trapped beneath the surface of the sand or gravel. In planted tanks there’s a fine balance between getting in there and uprooting plants, so be prepared to replant things if necessary.

You should keep going until you’ve removed 25% of the water in the tank. If there’s still more cleaning to be done you’ll want to handle it at a later date, moving too much water around at a time can stress the fauna in the tank.

Pay special attention to areas where the current may fall stagnant, such as under the edges of pieces of your hardscape. These areas can collect a lot of detritus that will continue to rot if left in place.

If this is your first major cleaning you may need to come back in a couple of days.

Save the last 3-4 gallons of removed water in your bucket. 

5. Cleaning Equipment

Filters, heaters, and even thermometers can all develop problems with algae. The glass on a heater’s bulb and other small pieces of equipment may not need to be cleaned in every tank, they tend to only attract brown algae.

Your filter is another matter.

Do not use tap water to clean your tank. If you’ve progressed this far along and didn’t save a bucket of water you need to dechlorinate the water used to clean out your filters. The last thing you want is chlorine killing all of your biological filtration.

A new sponge that’s never been exposed to soap can quickly clear off minor equipment components. I’ll often clean the exterior of filters as well, getting off any calcium stains or spilled food from the time in between cleaning sessions.

Clear the intake and output tubes of your filter. If you’ve been having trouble with the intake tube clogging, you can take this opportunity to stick a bit of sponge filter over it. It may lower the flow rate a bit but the intake will go longer without becoming 100% clogged.

Filtration is where you need to pay a bit more attention. I recommend the following protocols for differing media:

  • Sponges- Repeatedly dip to knock off loose debris, then run half of the sponge through your fingers to shake loose stuff that’s trapped inside. Try to preserve a portion of the brown stuff, since that’s made up of bacteria and nutrients needed to keep things chemically balanced in your aquarium.
  • Activated Carbon- Check to see if it’s time to replace the media. If not, rinse well in the bucket and return it to the filter. Activated carbon loses efficacy over time, so it’s important to keep track of when this stage was installed.
  • Ceramic Media- Rinse lightly but do not scrub or otherwise mess with it too much. If it’s loose media then I recommend bagging it before returning it to the filter but it’s not required.

If you have a canister filter there’s no need to dip the whole thing. Just open it and clean the components in the bucket. I’d also pour off the water contained inside and replace it to remove extra detritus. Do not use chlorinated water to refill your canister filter.

6. Refill Water and Replace Equipment

Replace the removed water volume in your tank with dechlorinated water when you’re done cleaning the equipment and get everything set up.

Remember that all aquarium filters need to be started wet. So pour some water in HOBs and make sure canisters are cleaned up and refilled before trying to start the pump again.

Fill the tank back to its original volume, or further if it was low on water. Ideally, you’d replace any evaporated water with distilled water but that’s impractical in the real world. You usually only need to get distilled water if you’ve lost more than 10% of a tank’s water level to evaporation.

I usually fill tanks until they’re behind the plastic bracket. This keeps a small spot where unsightly hard water stains won’t be seen while allowing you a bit of room to move in the tank without it spilling.

Get the equipment started again once you have the tank filled.

7. (Optional) Clean the Hood

If you have a glass hood, you can take this opportunity to clean it very well. You’ll want to use a 1:1 white vinegar to water solution and a razor blade or algae scraper.

Vinegar will break down the majority of light staining within seconds, while the razor blade will help “assist” the more stubborn bits in moving along.

Dry thoroughly before replacing the hood. You don’t want vinegar messing with the pH of your tank if you can avoid it.

8. Schedule the Next Cleaning

Tank maintenance can be approached in two ways.

You can wait until the tank is entirely out of hand and then clean it. This usually takes a few months between cleanings, doesn’t get rid of the most labor-intensive part (water changes), and generally means you’ll have to set aside a whole afternoon to handle the problem.

Or you can just come up with a regular maintenance schedule and go through the whole process in an hour or two regularly.

I usually deep clean my tanks and equipment once per month, about on time with the replacement of activated carbon filters. The rest of the maintenance is done on a weekly schedule or as needed.

With a regular schedule “as needed” only happens in emergency circumstances. You’ll save a lot of time and work by just switching to a regular schedule for tank maintenance and cleaning.

Cleaning Up for Good

Whether it’s a long-awaited deep clean or just a little bit of maintenance, knowing how to clean your fish tank properly is an important part of your skillset. It’s not complicated, but taking a systematic, regular schedule is the best bet for the long-term health of your aquarium.

So, get to it! A happy, beautiful, clean aquarium is a wonder to behold!