Annoying Algae: Keeping Algae Out of Your Hydro System

By Chris Bond
Published: March 8, 2022 | Last updated: March 8, 2022 12:59:33
Key Takeaways

Algae competes with your plants for nutrients and oxygen and can make a mess of your hydro system. Follow Chris Bond’s tips to keep it at bay and, should it become a problem, clean your equipment.

Like weeds in your garden or fleas on a pet, sooner or later you will probably find algae in your hydroponic system. A little is no cause for alarm; consider it a notice that a few tweaks need to be made. If you discover a lot though, you will need to act. Too much algae buildup Is detrimental to a hydroponic system and whatever you are growing in it.


Algae are simple, plant-like organisms. They require water, light, warmth, and a food source to thrive. These are the same things almost all living things need, including your crops. Since algae do not have roots, branches, or leaves, they must absorb all of these things directly and a hydroponic system is a great place to do so. Algae is naturally occurring and can pop up anywhere as their spores are all around us. You have undoubtedly seen any bucket or container of water left in the sunlight will form algae after a short time if ignored. While your hydroponic system is probably not being ignored, you can see how easily algae can seemingly appear out of nowhere.

algae in a hydro system


Why Algae is a Bad Thing for Your Hydro System

Besides being unsightly and sometimes emitting a bad smell as it decomposes, algae can wreak havoc on a hydro system in several ways. Since algae need what your plants need, they are competing for the same resources. This depletes your hydro system’s nutrient stores and can stress your desirable plants. This is not the worst part though. Algae also causes the dissolved oxygen levels in the water to drop.

As algae decompose, they rob the solution they are growing in of oxygen which in turn starves the roots of the plants you are trying to grow. This can create favorable conditions for diseases, such a Pythium, to invade. Decomposing algae also increases the carbon levels, alters pH levels, and can even release toxins into the system as it decomposes. Algae can also inadvertently be a food source for other unwanted microscopic pathogens and plant pests, such as fungus gnats and shore flies. Once algae take hold in your system, doing nothing is no longer an option.

Algae in a hydroponic system can also make a real mess of the mechanical operations. If not attached to a surface or plant, algae that is free flowing can find its way into any open pipe, tube, filter, pump, etc. From there it can reproduce and cause clogs or bog down the system so that it does not operate at proper capacity. This too will reverberate throughout your hydro system with negative repercussions.


algae in hydroponic system

How to Control Algae

Since algae thrive on the very conditions your crops do, it can be very difficult to control it once it has set up shop. A little bit can be tolerated, especially if it does not show up until the tail end of your current crop, or shortly before harvest time. When it is first noted, though, it will need to be monitored to make sure it does not get out of hand and harm your crop. Once it has gotten to the point where it must be dealt with, a thorough cleaning is the only reactive measure that will control it. This means your crop may need to be terminated. If it can wait until harvest, then very little will be lost. If it develops early on in your crop cycle, the crop will need to be sacrificed.


Every aspect of your growroom must be decontaminated and disinfected. This is does not just include the hydro system and all the pots, and media, but it also includes includes walls, floors, lights, vents, doors, and every other surface within the room. It is important to use new or disinfected brushes, sponges, and other cleaning equipment that has not previously been used to clean algae or other pathogens so you do not inadvertently reintroduce spores to your room or system. Regardless of your particular setup, the steps to control algae in your hydroponic system are pretty much the same.

Your system must be drained. You cannot reuse this nutrient solution or water. Make sure it is properly disposed of so it cannot re-infect anything. Then, every connection to pumps, aerators, pipes, etc., will need to be removed for cleaning. There are several options of cleaning solutions available on the market, both biological and chemical, but a good and effective standby is hydrogen peroxide. It is important that whatever you use is caustic enough to kill the algae but will leave no reside that will harm your next crop. Since algae is a form of plant life, this fact must be taken seriously. Use too weak a solution and the algae will quickly reform; use too strong a solution and your next crops will be damaged.

Once everything has been drained and thoroughly sanitized in your system and growroom, you will need to run a cleaning solution through your hydro system to kill anything that could not be reached during the sanitation process. Once that is done, drain the system again and run clean, preferably reverse osmosis or distilled water through your system to rinse it. Then, ideally you can let the growroom completely dry out and sit idle for a short time before starting your next crop. The longer you can wait to restart your hydro system, the better, but make sure everything is completely dry before refilling your system and starting your next crop cycle.

StonewoolUsing material like stonewool will keep your root zone wet, while keeping the top of the media dry.

How to Prevent Algae

Like so many other things in life, the best way to control or combat algae in your hydroponic system is to never have it to begin with. There are several precautionary or preventative steps that can be taken to reduce the chance of developing algae. Algae develops when conditions favor it. Making the environment inhospitable for algae while still giving your plants what they need is the key.

Algae needs light, as do your plants. What you can do is to try keeping light from shining onto your water and the grow media. This can be done in several ways. All sections and components of your hydroponic system (except for where your plants are) should be constructed of opaque material or otherwise be covered with a material that will not allow light to pass through. Make sure whatever material is chosen is at least 250 microns thick to block out UV light from passing through.

The very nature of a hydroponic system is counterintuitive to the concept of keeping your media dry, but algae does not form on dry surfaces. Using material like stonewool will keep your root zone wet, while keeping the top of the media dry. Other options can be as simple as raising the media higher than the water level so the tops can stay dry.

Barley straw is another option for algae control. Barley straw intended to prevent algae is generally sold in rafts. These rafts float atop your hydro solution or nutrient reservoir, if not covered. As the barley begins its decomposition process, it releases substances that prevent algal development and growth. It should be noted this is only an effective preventative measure if the proper levels of dissolved oxygen are present in your hydro solution.

Temperature control of your hydroponic water will also help to prevent the development of algae. Keeping the water temperature closer to 40°F (4.4°C) will prevent the development of most algae and still not be too cold for most hydro crops. If the temperature of your water rises above 57°F (14°C), it is conducive for the growth of some types of algae.

Lastly, making sure that your hydroponic system is as sanitary as possible will keep algae development at bay. Make sure your system has a quality filtration system and is checked and serviced regularly. This is true for both the water and the air in your growroom. Make sure as well that your system is thoroughly cleaned between crops. This will not only help to keep algae at bay, but it is good practice to keep a wide variety of pathogens from encountering your crops.

Read also:

Beneficial Algae

While finding algae in your hydroponic system means adjustments need to be made, researchers have found some examples of algae beneficial to hydroponic growing. Other types of algae have been used for nutrients for decades. Giant brown algae, a type of seaweed, can be used as plant supplements or in fertilizer. Other algae species have been found to release plant-growth regulators which can then be introduced into the hydroponic system. Still other types of algae produce anti-fungal and anti-bacterial substances that could be deployed into the root zone of plants through a hydroponic system.

Unless you are a phycologist (one who studies algae) and know you have a beneficial strain in your midst, you should probably go ahead and try to get rid of it.


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Written by Chris Bond | Certified Permaculture Designer, Nursery Technician, Nursery Professional

Profile Picture of Chris Bond

Chris Bond’s research interests are with sustainable agriculture, biological pest control, and alternative growing methods. He is a certified permaculture designer and certified nursery technician in Ohio and a certified nursery professional in New York, where he got his start in growing.

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