How To Clean A Planted Aquarium: Steps For Cleaning, Removing Algae and Grooming Plants

Fish keeping is a highly engaging hobby, and watching fish swimming around in a healthy tank is restful. But to keep an aquarium in good health, you need to clean it from time to time to remove dissolved wastes in the water, mulm in the gravel, and algae and biofilm growing on various surfaces.

However, plants in an aquarium will use waste products as a food source. As a result, how to clean a planted aquarium differs from how to clean a tank without plants, as you do not want to disrupt the delicate balance inside your planted aquarium. Keep reading to learn the step-by-step process to do the job correctly.

The Basic Principles Of How To Clean A Planted Aquarium

When cleaning an aquarium, you should not remove the fish, as you risk injuring and stressing them. You do not need to remove all the water to clean a fish tank – instead, you will only perform a partial water change. As a result, you can leave the fish in the tank.

You should never completely change the water in an aquarium. You will throw the chemical balance in your aquarium out of kilter and subject its inhabitants to nitrite and ammonia spikes that will kill them. Instead, do partial water changes every week, and clean your tank about once a month to remove algae, debris, and mulm on the surface of the substrate.

Partial water changes are necessary to replace lost minerals and trace elements and prevent the pH from falling too low and creating an environment that is too acidic for your fish. 

Replace around 10 to 15 percent of the water at any one time. Increase this amount to 20 to 25 percent in a heavily-stocked tank. Ensure that the new water stands for a day to let the chlorine dissipate, or use a water conditioner. When replacing the water, ensure it is at the same temperature as the water in the aquarium.

When you do your monthly clean-up of the aquarium, vacuum the hardscaping in the tank at the same time as you perform the partial water change. Clean your filter a few days afterward to avoid disrupting the community of beneficial bacteria in your aquarium too much.

Groom your plants weekly and do other essential plant maintenance tasks monthly.

Why Not To Clean The Substrate In A Planted Aquarium

Not only does gravel, pebbles, or another substrate in an aquarium enhance its aesthetic appeal and make it a more natural and less stressful environment for your fish, but it also provides an environment for beneficial bacteria to grow.

These beneficial bacteria are nitrifying bacteria, which convert nitrites in the water into nitrates. Cleaning your gravel by removing it from the tank and washing it will destroy these beneficial bacteria and reset the nitrogen cycle, like when all the water is replaced.

Moreover, a planted tank often has a layer of soil under the substrate that you should not disturb. If you do not have soil, detritus in the substrate may be your plants’ primary source of nutrients.

While you cannot let nitrates (and phosphates) build up too much in a tank, as they are harmful to fish and encourage the growth of algae, mulm and detritus in the substrate will decompose and be a source of nitrogen (and phosphorus) for plants. Therefore, you should not vacuum into the substrate if you have a planted tank.

Steps To Follow When Cleaning Planted Aquariums

Cleaning a planted aquarium may seem daunting, but when you break it down into steps, the task becomes doable.

1. Things To Switch Off Before Cleaning Your Aquarium

When cleaning your aquarium, the first thing to do is to switch off and unplug the heater, filter, and lights. If the lights are off and the tank is dim, it helps calm the fish and reduce their stress. 

2. Remove The Algae From Your Aquarium

Next, scrape any algae off the sides of your aquarium using an algae pad or scraper. While you can use a metal scraper on glass, you should use a plastic scraper if your tank is made of acrylic. For hard-to-remove beard algae, you may have to use a razor blade, a toothbrush, and plenty of elbow grease. 

When cleaning near the substrate, do not stir up lots of fine particles that will scratch your glass. You should never use chemicals or soaps, as these will kill your fish.

3. Siphon Your Aquarium To Clean It

Use a siphon to vacuum any large debris, uneaten food, and mulm off the surface of your substrate. Be careful around new plants that do not yet have a well-developed root system, as you could dislodge them. However, ensure that you hoover in beds of well-established plant cover that could be holding large amounts of detritus.

Siphon off around 10 to 15 percent of the water in the tank and replace it with dechlorinated water, i. e. perform a partial water change. While some people advise that you can change up to 50 percent of the water at this time, we recommend that you stick to a smaller percentage to avoid disrupting the balance of your aquarium. Siphon the replacement water into the tank to prevent disrupting the plants and substrate.

Stick a piece of sponge into the mouth of the siphon to prevent fish from getting sucked up.

4. Cleaning Plants And Hardscaping In Your Aquarium

If plants and hardscaping, such as rocks or ornaments, have debris, brush them off while leaving them in the aquarium. However, if algae are growing on your plants or rocks, you must remove them from the tank and clean them as detailed below. You can scrub algae off rocks under running water without ill effects on the stone, but you must use a more careful approach with plants to keep them healthy.

Scrub algae off gravel with a sponge, or use a bamboo toothbrush on pebbles. Do not use any form of soap to clean the plants or the hardscaping, as it is toxic to the fish.

5. Cleaning The Lid Of Your Aquarium

If your aquarium has a glass lid, water will condense on it, creating an ideal environment for molds to grow. Mold growth not only looks unsightly but is also toxic and could make your fish sick. Ensure that you wipe the water off the lid of your tank.

6. Switch On Again After Cleaning Your Aquarium

Once you have cleaned your aquarium, check for any large bits of debris and scoop them up with a net. Check that your hardware is in good order, and switch the lights, heater, and filter back on again. Be patient, as small particles of dirt will be suspended in the water, and your filter will take a couple of hours to clear them.

7. Check Your Aquarium’s Water Parameters After Cleaning

After cleaning your tank, and every time you do a partial water change, check the water parameters (nitrate and ammonia levels, hardness, and so forth) to ensure that the chemistry of your tank is still in balance. Watch your fish for a couple of days after cleaning the tank to see that they are okay.

8. How To Clean Your Aquarium Filter

A few days after cleaning your aquarium, switch off your mechanical filter, and open it up. Scrub debris off your filter to reduce algal build-up, and remove any wayward snails lurking here. Clean your filter regularly – ensure that particulate organic matter does not build up, as it will rot and affect your water quality.

How To Remove Algae From Aquarium Plants

If you have algae growing on your aquarium plants, and your snails or algae-eating fish cannot keep it under control, you will have to clean it off. Try rubbing the algae off the plant while it is still in the tank. If the plant has a large amount of algae, remove the plant from the tank and use an algae pad to scrub the algae off it gently.

How To Clean A Planted Aquarium

Bleach Treat Aquarium Plants To Remove Algae

If a plant is severely overgrown with algae, it will die. In this case, you should consider the more extreme treatment of bleaching it. Remove it from the aquarium and soak it for a maximum of five minutes in a ten percent bleach solution.

Once you have soaked the plant, remove it from the bleach solution and gently rub the algae off. Then soak the plants for about ten minutes in clean, conditioned water to remove the bleach before returning them to the tank.

How To Groom Your Aquarium Plants

Once a week, groom your aquarium plants. Trim off dead or dying leaves on broadleaf plants such as Cryptocorynes and Anubias and cut and replant bunch plants that are becoming leggy or shedding their lower leaves. Trim ground-cover plants such as mosses with scissors and skim off surface plants such as duckweed and hornwort to allow light to reach plants lower down.

Once a month, remove or thin out any fast-growing plants that threaten to swamp smaller, slower-growing ones.


Planted aquariums require regular cleaning and maintenance just as tanks with no plants do. However, as you can see the method varies somewhat in that you will want to leave some elements, such as substrate, alone to preserve healthy bacteria. Additionally, you will have to manage algae on both plants and the tank itself, as well as groom your plants. Following these steps for how to clean a planted aquarium will hopefully help you streamline the process and not forget any important steps.

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