Nutrient Deficiencies in Aquaponics: How to Recognise and Fix Common Problems Naturally
Understanding Nutrient Deficiencies in Aquaponics
When your plants start turning yellow in aquaponics systems, curling at the edges, or showing spots on their leaves, it’s easy to assume something is wrong with your fish or water quality. But in most cases, you’re seeing early signs of aquaponics plant deficiencies.
In aquaponics, all nutrients come from a living source, your fish, so balance can shift depending on feeding rates, fish numbers, pH levels, system maturity, or even the time of year.
The good news? Most aquaponics nutrient deficiencies are easy to identify and correct once you understand what your plants are telling you.
Over the years, I’ve found that most aquaponics plant problems come back to pH imbalance and iron deficiency, and both are simple to fix once you know what to look for.
Quick Signs of Nutrient Deficiencies in Aquaponics
Yellow new leaves with green veins → Iron deficiency
Brown or yellow leaf edges → Potassium deficiency
Twisted young leaves or blossom-end rot → Calcium deficiency
Yellowing older leaves → Magnesium or nitrogen deficiency
Slow overall growth → Often nitrogen related
Use this as a starting point before making any changes to your system.
What Causes Nutrient Deficiencies in Aquaponics?
Unlike traditional gardening, aquaponics doesn’t use chemical fertilisers. Nutrients are created through the natural breakdown of fish waste by beneficial bacteria, then absorbed by plants through their roots.
If you’re still learning how this process works, read about the natural breakdown of fish waste by beneficial bacteria.
Deficiencies usually appear when:
The system is new, and the bacterial cycle isn’t fully established.
Fish numbers or feeding rates are too low to produce enough waste.
pH levels are too high or too low, causing nutrient lockout.
Certain nutrients (like iron, potassium, and calcium) are naturally limited in aquaponics systems and may need topping up with safe, natural supplements.
If you’re unsure whether your stocking levels are appropriate, you may also want to read about choosing the right fish for your aquaponics system.
What Is Nutrient Lockout?
Even if nutrients are present in your water, plants can’t absorb them properly if the pH is outside the ideal range. This is called nutrient lockout in aquaponics.
At high pH (above 7.5), essential elements like iron, manganese, and zinc become chemically unavailable.
At low pH (below 6.5), calcium, magnesium, and potassium uptake can drop.
Maintaining a stable pH between 6.8 and 7.2 keeps your plants happy and allows them to access everything they need. Always adjust pH slowly and naturally using buffers like potassium bicarbonate or calcium carbonate.
Common Aquaponics Nutrient Deficiencies and How to Fix Them Naturally
1. Iron Deficiency
Symptoms: New leaves turn pale yellow while veins stay green (interveinal chlorosis).
Common in: Leafy greens and herbs.
Cause: High pH causing nutrient lockout.
Fix: Add chelated iron (Fe DTPA or Fe EDDHA) directly to your system every few weeks until colour returns.
2. Potassium Deficiency
Symptoms: Yellow or brown leaf edges, weak stems, slow fruiting or flowering.
Common in: Tomatoes, capsicums, strawberries.
Fix: Add potassium bicarbonate (also helps stabilise pH) or use natural sources like worm juice made with banana skins, which are rich in potassium.
3. Calcium Deficiency
Symptoms: Young leaves curl or twist; fruit may develop blossom-end rot in aquaponics systems.
Common in: Tomatoes, lettuce, and spinach.
Fix: Use crushed eggshells or shell grit in your system for a slow calcium release. You can also blend eggshells into worm juice for an extra calcium boost.
4. Magnesium Deficiency
Symptoms: Older leaves turn yellow between veins, but veins remain green (similar to iron deficiency, but on lower leaves).
Fix: Add Epsom salt (magnesium sulphate) at 1 teaspoon per 100L (26 gal) of system water. Always dissolve fully before adding, and only supplement after confirming magnesium deficiency to avoid overcorrecting.
5. Nitrogen Deficiency
Symptoms: Overall yellowing of older leaves and slow plant growth.
Cause: Not enough fish or underfeeding.
Fix: Gradually increase feeding or fish numbers if your system can handle it. In early stages, add a small amount of fish-safe organic nitrogen such as compost tea or worm castings.
If your system is brand new, this may simply be part of the cycling process.
Natural Ways to Boost Nutrients
Sustainability is one of the biggest strengths of aquaponics. Instead of reaching for synthetic fertilisers, you can naturally enrich your system with gentle, home-based supplements.
Worm Juice
Rich in potassium (from banana skins) and calcium (from eggshells), worm juice provides a broad range of minerals. Add a small cup weekly to your grow bed or sump to help prevent deficiencies.
Comfrey Tea (Foliar Spray)
Comfrey leaves are naturally high in potassium and trace elements. Soak chopped leaves in water for 5–7 days, strain, and use as a foliar spray on leaves once a week.
Seaweed Extract (Low Sodium)
Adds potassium, magnesium, and trace minerals. Use sparingly and check for added nitrogen or urea before use.
Crushed Coral or Shell Grit
Slow-release calcium source that also helps buffer pH gently over time.
How to Prevent Nutrient Deficiencies
Keep pH Balanced (6.8–7.2)
Nutrient lockout is the most common hidden cause of aquaponics plant problems. Check pH weekly and adjust slowly.Feed a Quality Fish Food
High-protein, aquaculture-grade feed supports both fish health and plant nutrition.Add Natural Supplements Regularly
A small, consistent routine (like weekly worm juice and monthly chelated iron) prevents most deficiencies.Stock Wisely
Understocked systems often lack nutrients; overstocked systems struggle with waste. Around 20–25L (5–7 gal) of water per fish is a safe guide for beginners.Watch Water Temperature
Colder water below 18°C (64°F) slows bacterial activity and can lead to nutrient imbalance. Keep systems gently aerated in winter.
Diagnosing Aquaponics Plant Problems: Step-by-Step
Check your pH and temperature first.
Note which leaves are affected (new or old).
Compare symptoms to the list above.
Adjust gradually, avoid big swings or multiple fixes at once.
Give plants time to recover.
Aquaponics troubleshooting is about small, steady corrections rather than dramatic interventions.
How to Maintain Nutrient Balance in Aquaponics
Aquaponics nutrient deficiencies are simply signs that your system needs a small adjustment. Once you understand nutrient lockout and add a few natural supplements, your aquaponics setup becomes remarkably self-sustaining.
Think of your plants as storytellers. They will always show you what your system needs next. Listen carefully, nurture the balance, and your fish and plants will thrive together.
Learn More About Iron Deficiency in Aquaponics
If you’re just getting started and want a deeper explanation of iron deficiency in aquaponics, watch this beginner-friendly breakdown:
Unravelling the Mystery: How Iron Deficiency Affects Aquaponics Growth for Starters
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.
