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How To Clean Algae From Aquarium Rocks: Risks & FAQs

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By Lindsey Stanton


Algae might be a naturally growing plant of sorts, but that does not mean that you want it in your aquarium. Algae do not always bloom in every aquarium, but at one point or another, chances are that you will see algae in the tank.

It can be caused by various factors, but once it develops, you might have a hard time getting rid of it. How to clean algae from aquarium rocks is what we will discuss today. We will also go over some algae prevention tips as well but let’s first look at what problems algae can cause to your tank.

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Problems Caused By Algae in Aquariums

There are a few things that you need to beware of when it comes to algae and your aquarium. Now, it is not like it is the worst thing in the world for your fish, but it definitely is not beneficial either. What are some of the main problems caused by an algae bloom in your fish tank?

Lack of Oxygen

One of the biggest problems caused by algae blooms is that they eat up a ton of oxygen in the tank. Your fish and plants both need oxygen to survive. Too much algae can cause a significant decrease in water aeration and oxygenation, which is not good for plants or fish.

green algae aquarium
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Lack of Nutrients

This is especially important for your aquarium plants. The more algae in the water, the more nutrients it sucks out of the water. This can be a real problem for many plants that require the absorption of nutrients through the substrate and water column.


This does not happen very often, but certain types of algae can be toxic to fish.

Cloudy Water

One of the first and most obvious drawbacks to having algae in the tank is that it makes the water cloudy and makes everything look really dirty. The water will be milky and discolored, and your decorations will get covered in it too.

goldfish in dirty unclean tank
Image Credit: Chaikom, Shutterstock

Filter Issues

Algae can be bad for filters; it can clog the tubing and cause media to be used up way too quickly. At the same time, the filter you have might not be able to keep up with the increased demand that it is faced with due to a big algae bloom.


How to Clean Algae From Aquarium Rocks:

Whether it is white, black, green, blue, or red algae, and whether it looks stringy, mossy, or puffy, you need to get rid of it if you see it growing in your aquarium. It may only look like a little bit today, but given the right conditions, you might wake up tomorrow to a fish tank full of it.

If you see it growing on rocks and other decorations, you need to clean it off ASAP, and you should take the right steps to correct the underlying issue. Here’s a step-by-step guide on how you can effectively clean algae from your aquarium rocks and other decorations in the tank.

How to Get Algae Off Rocks

  1. Remove the decorations from the tank. Make sure to go slowly and remove them one at a time; removing too many at once can cause stress to your fish. Make sure not to shake the decorations in the water. You don’t want to knock off any algae and release it directly into the water.
  2. You should move all live plants to the corner of the tank so that the substrate is exposed. Use an aquarium siphon and gravel vacuum to clean as much debris from the rocky substrate as possible.
  3. Now, take the rocks and other aquarium decorations. Place them in a pot of water that has reached boiling temperature and let them soak for about 20 minutes. This should kill off most of the algae present on the rocks and decorations.
  4. Get a new toothbrush and scrub the rocks and decorations. There is no need to be really gentle. Get into all of the corners and nooks in your rocks and decorations, removing as much algae as possible.
  5. Take a bucket and create a bleach solution. The solution should be 95% warm water and 5% bleach. Soak the rocks in the bleach mixture for around 5 minutes, using gloves to ensure you don’t burn your hands. Now take the toothbrush and scrub the decorations again.
  6. Make sure to rinse the decorations thoroughly, first with cool water and then with warm water. If there is any bleach on the rocks or decorations when you put them back in the tank, it can cause serious health risks for your plants and fish.
  7. If you are worried about chlorine in the water, you can get a bucket of water, use a de-chlorinator with it, and soak the rocks in the dechlorinated water. Now they should be ready to be put back into the tank.
  8. Put the rocks and decorations back into the tank.

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Causes of Algae Blooms – and the Solutions

Before we get into cleaning algae off of aquarium rocks and how to get rid of it within the tank, it is vital to know what the underlying causes of the algae bloom are. After all, it needs certain conditions for growth.


Algae love to eat nitrates as well as phosphates. It is one of the main food sources they use to grow. If you have an overstocked tank, chances are that there are a lot of nutrients in the water which will aid algae growth.

Having too many fish will cause ammonia and nitrate spikes, which algae does not mind at all. You need to do everything you can to reduce nitrate levels (the right plants also help). The easiest way to go is with denitrifying solutions that are designed for aquariums.

bristlenosed pleco
Image Credit: TTONN, Shutterstock

Inadequate Filtration

If you don’t have a good filter, it can also cause algae blooms to occur. If you have good mechanical filtration, it should filter out a lot of the algae. At the same time, a good biological filtration system should be able to take care of nitrates and other algae food sources.

However, if your filtration unit is not good enough or it is not functioning properly, it won’t remove these nutrients from the water, thus allowing algae to bloom.

Dirty Water

Make sure to clean your fish tank on a regular basis. This means removing dead fish, decaying plants, and old food. All of those things, as they decay, give off nutrients that algae will use to grow.

You need to clean decorations, rocks, plants, the glass itself, and the substrate. Making regular water changes and regularly cleaning the aquarium will help prevent algae blooms.

Old Lights

We don’t want to get too deep into the science of it here, but aquarium lights change the spectrum of light they release as they age. It is shown that older aquarium lights tend to favor algae growth, especially the really strong ones.

It’s best to replace aquarium lights every 6 to 8 months. Different lights have different lifetimes, so make sure to do some research on the specific lights you have.

fish inside a dark aquarium
Image Credit: Pixabay


Heat is not the sole cause of algae growth, but when combined with some of the above aspects, a really warm aquarium is definitely a good home for algae. Make sure that the water is warm enough for your plants and fish, but don’t keep it at an excessively warm temperature either.

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Will Boiling Rocks Kill Algae?

If you have algae on rocks in your aquarium, you want to get rid of it as fast as possible. Now, some people wonder whether or not boiling rocks is enough to kill algae.

The answer here is that no, boiling your rocks will not kill the algae. It may sound weird that the high temperature does not kill the algae, but it may actually worsen the situation. Boiling rocks with algae may actually cause the algae to burst and release toxins into the water.

red cherry shrimp and moss balls
Image Credit: Ian Grainger, Shutterstock

How Do You Remove Brown Algae From Rocks?

Yes, cleaning aquarium rocks is something you will have to do regularly in order to remove algae, physical debris, and a number of other contaminants. The easiest way to remove algae, such as brown algae, from aquarium rocks is to first scrub them down with a brush to remove as much of it as you can by hand.

Next, you want to create a solution of around 90% water and 10% bleach (brown algae is tough, so you will want a good deal of bleach). Then, soak the rocks in this solution for about half an hour, then scrub them down again with your brush, and finally rinse them off well.

Can You Use Bleach to Clean Aquarium Rocks?

Yes, you can use bleach to clean aquarium rocks, and when it comes to rock algae, it is actually the most effective way of getting rid of it. Always be sure to make a diluted solution of no more than 10% bleach and 90% water, and rinse off the rocks thoroughly afterward. Remember, you do not want to get any bleach residue in your aquarium.

How Do You Clean New Aquarium Rocks?

If you feel the need to do so, which you probably should, as new aquarium rocks can be quite dirty, simply boil the rocks for about 20 minutes to remove bacteria and parasites.

Follow that up with a bleach bath, as discussed above, since it will remove the remaining contaminants. Finally, as always, be sure to rinse the rocks thoroughly so you don’t get any bleach into the fish tank.

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Wrapping Up

Cleaning algae off of aquarium rocks is really not that hard, but it takes some time and effort. The best way to ensure that you don’t have algae in your aquarium is to take care of the underlying causes right from the get-go. However, if you find that there is a lot of algae in your aquarium, our tips are good methods to keep in mind.

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