Algae in Aquaponics: Causes, Types, and How to Control It Naturally
Understanding Algae in Aquaponics
If you’ve ever noticed green slime on your fish tank walls or a green film across your grow bed, you’re not alone. Algae in aquaponics systems is one of the most common (and persistent) challenges, especially in smaller setups or those exposed to sunlight.
A little bit of algae is normal in aquaponics, but excess algae can cause problems if it’s left unmanaged. Let’s look at what causes it, the types you might find, and how to manage it naturally, both in glass indoor aquariums and outdoor systems.
If you’re new to aquaponics or unsure about any of the terms used in this article, you can refer to this aquaponics glossary for beginners, which explains key concepts in plain language.
What Is Algae and Why Does It Grow in Aquaponics Systems?
Algae are simple, plant-like organisms that love three things: light, nutrients, and water, all of which are naturally present in aquaponics systems.
Unfortunately for us, aquaponics provides all three, which is why algae growth is so common in both indoor and outdoor aquaponics setups. If you’re just starting out, following a well-balanced setup from the beginning, like this step-by-step guide on how to build a small aquaponics system at home, can help reduce algae issues before they become a problem.
Algae flourish in aquaponics systems when:
Sunlight or grow lights reach nutrient-rich water.
Fish waste and uneaten food build up in the system.
Warm temperatures speed up growth.
In small amounts, algae can help filter the water and even provide snacks for some fish. But when it grows out of control, it can unbalance your entire ecosystem.
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Why Too Much Algae Is a Problem in Aquaponics
It uses oxygen at night
During the day, algae photosynthesise and release oxygen, but at night they switch to consuming it instead. This can lower oxygen levels, increase stress, or even suffocate fish, particularly in small aquaponics systems or indoor fish tanks.It clogs your plumbing and filters
Floating algae and biofilm can block pipes and slow water circulation in aquaponics systems, reducing overall system efficiency.It competes with your plants
Algae absorb the same nutrients your vegetables need to grow, leaving less available for your crops.It makes the system look dirty
Especially in glass aquariums, it can coat the walls or water surface, turning clear water into green soup.
Common Types of Algae in Aquaponics
Green Water (Free-Floating Algae)
Makes your water cloudy or green, often from too much direct sunlight hitting nutrient-rich aquaponics water.Green Spot Algae
Forms small, stubborn patches on tank glass or plumbing.String or Hair Algae
Looks like green strands or slime that cling to grow beds or roots in aquaponics grow beds.Brown Algae (Diatoms)
Common in new systems, especially indoors; appears as a dusty brown coating that often fades as your system matures.
How to Control Algae in Aquaponics Naturally
1. Limit Light Exposure
Shade outdoor fish tanks or cover them with recycled corrugated plastic, hessian, or shade cloth.
For indoor systems, avoid placing tanks near windows or under constant light.
Use grow lights on timers (8–10 hours a day) instead of leaving them on 24/7.
2. Balance Feeding and Filtration
Overfeeding fish leads to excess nutrients, the perfect fuel for algae growth in aquaponics systems.
Feed what your fish can eat within 2–3 minutes.
Clean mechanical filters regularly and check that your biofilter is healthy.
3. Add Algae-Eating Companions
Depending on your setup size:
Outdoor systems: Silver Perch, Jade Perch, or Tilapia will graze on algae.
Indoor systems: Bristle nose Catfish, Otocinclus, or freshwater shrimp can help.
Avoid introducing species that don’t suit your climate or tank size.
4. Keep Water Temperature Steady
Cooler water discourages rapid algae growth in aquaponics. Use shading, air stones, and water movement to reduce heat.
5. Clean and Observe Regularly
Wipe tank glass weekly (a magnetic scraper works well).
Manually remove string algae before it spreads.
Check for blocked pipes or slow water flow.
Why Am I Getting Algae on My Grow Bed?
If you’re noticing a green or brown film forming on top of your grow bed media, that’s algae, too, and it’s common in aquaponics grow beds, especially outdoors or under strong light. In many cases, algae issues can be linked to grow bed design or drainage, which is why choosing the right grow bed for your aquaponics system is so important.
It happens because:
Water is sitting on the surface instead of draining fully.
Sunlight is hitting wet media directly, which encourages algae growth in aquaponics grow beds.
Nutrients from the water film encourage growth.
Here’s how to fix it:
1. Check Your Water Level
The top 1–2 cm of your grow bed should stay dry.
If water is constantly visible, lower your standpipe or adjust your flood-and-drain cycle.
2. Add Shade or Cover the Bed
Use recycled materials such as:
Bamboo mats or old hessian bags,
Lightweight floating covers (like perforated plastic),
Shade cloth over the grow area.
This blocks light while still allowing airflow.
3. Increase Plant Coverage
The more plant canopy you have, the less sunlight hits the grow bed surface.
Fast-growing leafy greens like basil, mint, or spinach can act as a natural shade.
4. Stir or Rinse Occasionally
If algae has built up on clay balls or gravel, gently rinse them in system water (never tap water) during maintenance.
Avoid cleaning too aggressively; you don’t want to disturb beneficial bacteria deeper in the bed.
5. Encourage a Natural Balance
A small amount of surface algae won’t harm your system. It’s only a problem if it starts to form thick mats or smell. When your water flow, light, and planting density are balanced, the algae will naturally reduce.
Watch: How to Get Rid of Algae in Aquaponics Grow Beds
If grow bed algae is your main challenge, this short video walks you through simple, practical fixes you can apply straight away.
Should You Use Algae Killers in Aquaponics?
Avoid them completely when dealing with algae in aquaponics systems. Chemical treatments or UV sterilisers may harm the bacteria that keep your system stable.
Natural control methods, like shade, system balance, and a few algae-eating fish, are always the best option.
A Natural Part of the Ecosystem
Algae in aquaponics isn’t your enemy; it’s a messenger.
It tells you your system has light, nutrients, and warmth in abundance. By learning to interpret these signs and adjust your balance, you’ll find your aquaponics water becomes clearer, your plants thrive, and your fish stay happy.
Frequently Asked Questions About Algae in Aquaponics
Is algae bad in aquaponics?
Algae is not automatically bad in aquaponics. In small amounts, it is a natural part of the ecosystem and can even help use up excess nutrients. Problems only occur when algae grows out of control, reducing oxygen levels, competing with plants, or clogging pipes and filters.
Why is my aquaponics water turning green?
Green water in aquaponics is usually caused by free-floating algae. This happens when nutrient-rich water is exposed to too much sunlight or grow light. Reducing light exposure, improving filtration, and balancing feeding will usually clear the water over time.
How do I stop algae from growing in my aquaponics system?
The best way to stop algae in aquaponics is to focus on balance rather than elimination. Limiting light exposure, avoiding overfeeding, keeping water moving, and cleaning regularly will naturally reduce algae without harming fish, plants, or beneficial bacteria.
Should I remove all algae from my aquaponics system?
No. Trying to remove all algae can actually do more harm than good. A small amount of algae is normal and healthy. The goal is to manage algae growth, not eliminate it completely, so your system stays stable and balanced.
Learn More About Aquaponics
Check out the COURSES page to learn how you can get started with aquaponics now. Click HERE.
Want to get your Eyes and Hands on the FREE Online Aquaponics Essentials Course?
This is a great free resource to really understand how aquaponics is a sustainable ecosystem that will grow your organic food is a productive way.
You learn how all the 'parts' make up the 'whole', and helps to give you the foundations of understanding aquaponics.
Sign up HERE
Check out my YouTube Channel 'Candy The Aquaponics Lady'
Aquaponics is an ecosystem, and with anything it takes time to learn how it works. So, sit back and binge watch my 'how to' playlist and the 'Water Quality Made Simple' Playlist, and learn the next steps in your aquaponics system as you create the ecosystem.
Here are the next 2 videos I recommend you watching to create your ecosystem ~ before you add any fish
How Aquaponics Works as an Ecosystem
Why aquaponics is the best form of gardening for you
Learn More About Aquaponics
Check out the COURSES page to learn how you can get started with aquaponics now. Click HERE.
Want to get your Eyes and Hands on the FREE Online Aquaponics Essentials Course?
This is a great free resource to really understand how aquaponics is a sustainable ecosystem that will grow your organic food is a productive way.
You learn how all the 'parts' make up the 'whole', and helps to give you the foundations of understanding aquaponics.
Sign up HERE
Want to help out (donate some fish food) and Feed my Fish?? (They don't drink coffee)
Candy Alexander is a dedicated aquaponics enthusiast with a wealth of formal training in aquaculture. Over the past 15 years, Candy has been deeply immersed in both commercial and backyard aquaponics, honing her skills and expertise in this sustainable farming method.
Candy's passion lies in making aquaponics accessible to everyone. With a mission to simplify aquaponics, she believes that anyone can embark on this sustainable journey.
She encourages those new to aquaponics to "kick the tires" without a significant financial investment. Her guidance focuses on helping people start their aquaponics journey with small-scale systems, ensuring a low barrier to entry for newcomers.
Candy shares practical tips, step-by-step guides, and personal stories to inspire and guide readers on their aquaponics adventure. Whether you're a seasoned farmer or a curious beginner, Candy Alexander is your go-to source for simplifying aquaponics and fostering a sustainable gardening experience.
