If you're running an aquaponics system, you're already tapping into one of the most sustainable ways to grow fresh food. But what if you could take that system one step further, increasing yield, reducing pests, and creating a healthier ecosystem, simply by choosing the right plant combinations?
That’s where companion planting in aquaponics comes in.
Traditionally used in soil-based gardening, companion planting focuses on growing certain plants together that benefit one another. The idea is simple: some plants can enhance nutrient uptake, repel pests, or improve the flavor and growth of their neighbors.
But does this principle apply in aquaponics?
Yes, and it can be even more effective when done right.
In this blog, we’ll explore the best companion plant pairings for aquaponics, which combinations to avoid, and how to design your grow beds or towers for maximum harmony and efficiency. Whether you’re growing in a media bed, raft system, or vertical tower, this article will help you build a healthier, more productive aquaponic garden.
What Is Companion Planting in Aquaponics?
Companion planting is the strategic pairing of plants that grow well together and support one another’s development. In traditional gardening, this typically means selecting combinations that share nutrients well, deter harmful insects, or attract pollinators.
In aquaponics, while there's no soil involved, the concept still holds value, perhaps even more so.
Because all plants share a common water source, root zone, and nutrient stream, choosing mutually beneficial plant combinations can help balance the system. Certain herbs like basil, oregano, and chives emit strong aromas that naturally repel pests, a huge bonus in chemical-free systems. Leafy greens like lettuce and kale are fast-growing and don’t compete heavily for space or light, making them ideal companions for slower, bushier crops.
Benefits of Companion Planting in Aquaponic Systems
Here are the top advantages of pairing plants strategically in your aquaponics system:
1. Natural Pest Control
One of the benefits with companion planting is organic pest prevention. Aromatic herbs like basil, oregano, dill, and chives naturally repel common pests like aphids, whiteflies, and spider mites. When planted near vulnerable crops (like lettuce or peppers), they act as plant-based protectors.
Example:Oregano near bell peppers can help deter aphids and spider mites without disrupting the pH or nutrient cycle in your system.
2. Enhanced Nutrient Uptake and System Balance
Pairing plants with complementary nutrient needs helps prevent one crop from dominating or depleting specific nutrients.
For instance:- Fast-growing leafy greens (like kale or Swiss chard) absorb nitrogen quickly
- Herbs (like basil or thyme) have moderate nutrient demands and won’t compete aggressively
This creates a more stable and nutrient-balanced aquaponic environment, reducing stress on your biofilter and improving overall system health.
3. Maximized Grow Space and Light Use
Companion planting lets you mix crops by height, root depth, and growth habit, meaning more production per square foot.
Example: In a media based, plant basil (short and bushy) under taller tomato plants to use vertical space efficiently.
This layering approach also reduces light competition and prevents crowding, which is crucial in densely packed grow beds or vertical systems.
4. Healthier Ecosystem with Less Maintenance
A diverse planting strategy leads to a more resilient aquaponic system overall. When plant pairings are chosen well:
- Pest infestations are less likely to spread
- Nutrient levels remain more stable
- Plants are less prone to disease and deficiency
This translates to less maintenance and troubleshooting for you, and a healthier, more efficient aquaponic garden over time.
Top Companion Plant Pairings for Aquaponics
Below are some of the best companion plant combinations that work especially well in media beds, raft systems, and vertical grow towers.
1. Lettuce + Basil
Best For: Raft System or Deep Water Culture (DWC), and NFT
- Why it works: Lettuce is a fast-growing leafy green that absorbs nutrients efficiently. Basil, a strongly aromatic herb, naturally repels aphids and whiteflies.
- System Tip: Both plants are shallow-rooted and thrive in high-oxygen nutrient flow environments like NFT or raft beds.
2. Tomatoes + Marigolds
Best For: Media Based, Vertical Systems
- Why it works: Marigolds help repel nematodes and whiteflies, offering natural pest deterrence in systems where tomatoes are vulnerable.
- System Tip: Tomatoes have heavier nutrient demands; ensure your fish stocking and biofilter can support fruiting crops.
3. Peppers + Oregano
Best For: Media Based
- Why it works: Oregano acts as a living mulch and deters aphids, spider mites, and small beetles, common pests in enclosed systems.
- System Tip: Peppers do best in warm, stable systems with plenty of light. Prune oregano to keep airflow open.
4. Cucumbers + Dill
Best For: Media Based, Vertical System
- Why it works: Dill attracts beneficial insects like parasitic wasps and ladybugs, which can keep aphids and mites in check, especially in greenhouse aquaponic setups.
- System Tip: Train cucumbers vertically to reduce space conflict and ensure proper light exposure for both crops.
5. Kale + Chives
Best For: Media Baseds, Raft System
- Why it works: Chives help deter fungal gnats and aphids, common issues in wet environments.
- System Tip: Both crops enjoy cool, nutrient-rich water, perfect for systems with moderate fish loads.
6. Strawberries + Thyme
Best For: Vertical Systems, NFT Channels
- Why it works: Thyme deters worms and slugs, helping protect strawberries naturally. It also emits a scent that masks the sweetness of the fruit, which can deter insect pests.
- System Tip: Keep this pair in a well-lit vertical system and monitor for moisture level consistency.
System Design Tips for Companion Planting
Even the best plant pairings will fall flat without a system that supports their needs. Whether you're using media baseds, raft system, NFT channels, or vertical towers, strategic layout and planning are essential to get the most out of companion planting in aquaponics.
Below are key design principles to guide your companion planting setup.
1. Group Plants by Nutrient Needs
Just like fish stocking rates, plants have nutrient requirements that must be balanced across the system. Grouping plants with similar feeding demands prevents one type from dominating nutrient uptake, especially in recirculating systems.
Try this:
- One grow bed: Mix lettuce, kale, and Swiss chard (nitrogen-loving leafy greens)
- Another bed:Group tomatoes, peppers, and basil (fruiting crops with higher phosphorus and potassium demands)
Tip:Rotate heavy feeders and light feeders seasonally to help maintain nutrient equilibrium in long-running systems.
2. Stagger Plant Heights for Light Efficiency
In tightly packed aquaponic beds, taller crops can shade out lower-growing plants. Companion planting works best when you stagger plants by height so they share light instead of competing for it.
Example layout:
- Back row:Tomatoes or cucumbers on a trellis
- Middle row: Basil, oregano, or dill
- Front row: Lettuce, arugula, or small leafy greens
This approach improves both light access and airflow, reducing the risk of mildew and rot.
3. Use Grow Zones for Better Root Compatibility
Different crops have different root behaviors. Some spread aggressively, while others stay compact. Creating root zones, even within the same media bed can prevent crowding and boost growth.
How to do it:
- Use plant net pots or grow collars in raft systems to isolate root zones.
- In media beds, place root-bound herbs like thyme and oregano at bed edges to limit their spread.
- Keep deep-rooted plants like beets in the center where there’s more media depth.
4. Rotate Crops Strategically
Crop rotation isn't just for soil! In aquaponics, rotating your plant types seasonally (or by nutrient group) helps avoid nutrient depletion, root buildup, and pest adaptation.
Sample rotation plan:
- Season 1: Lettuce + basil + tomatoes
- Season 2: Kale + chives + peppers
- Season 3:Swiss chard + dill + cucumbers
Rotate in sets of companion crops to keep the microbial balance in your grow bed healthy.
5. Follow Smart Aquaponic Plant Spacing
Overcrowding leads to competition and disease. Even compatible plants needs space, especially in high-humidity systems like greenhouses or covered setups.
Spacing tips:
- Lettuce:6–8 inches apart
- Tomatoes:12–18 inches apart (train vertically)
- Herbs:8–10 inches (denser spacing for chives, wider for basil)
- Root crops (like beets):4–6 inches, with depth
Rule of thumb:Space plants according to their mature size, not seedlings. Use vertical trellising where possible to maximize airflow and prevent contact rot.
Troubleshooting Common Companion Planting Issues
Even with the right companions, things can go sideways in an aquaponics system. Here are the most common companion planting issues in aquaponics, plus how to troubleshoot them effectively.
Problem 1: Stunted Growth in One or More Plants
Symptoms:
- One plant in a pairing isn’t thriving
- Leaves appear small, yellowing, or pale green
- Growth seems halted despite healthy-looking neighbors
Likely Causes:
- Nutrient competition — A heavy feeder is starving a lighter one
- Incorrect spacing — Plants too close together are battling for light or root space
Solutions:
- Rearrange plants so they’re grouped by nutrient demand
- Check and adjust plant spacing based on mature size
- Consider moving underperforming plants to another grow zone or media bed
Problem 2: Root Zone Overcrowding
Symptoms:
- Slowed nutrient uptake
- Water flow obstructions in NFT/DWC
- Algae growth near net cups or plant collars
Likely Causes:
- Companion plants have incompatible root sizes
- Aggressive root systems (like mint or rosemary) spreading too far
Solutions:
- Prune roots regularly in raft system and NFT systems
- Avoid combining deep-rooted crops with shallow-rooted ones in confined beds
- Use mesh pots or barriers in media beds to isolate root zones
Problem 3: Pest Pressure on One Crop in a Pairing
Symptoms:
- One plant consistently attracts aphids, whiteflies, or spider mites
- Infestation spreads despite using pest-deterring companions
Likely Causes:
- Overreliance on “helper” plants like basil or marigold
- Lack of airflow or humidity pockets due to overcrowding
Solutions:
- Manually inspect and isolate affected plants
- Increase air circulation using fans or by adjusting layout
- Use IPM (Integrated Pest Management) tactics like neem oil, ladybugs, or sticky traps
Tip:Companion planting reduces pest pressure, it doesn’t eliminate it entirely. Keep up your regular pest scouting and management schedule.
Problem 4: Uneven Growth or Wilting in NFT and Vertical Towers
Symptoms:
- Top or bottom plants thrive, others wilt or discolor
- Roots dry out or rot despite proper watering schedules
Likely Causes:
- Inconsistent water distribution
- Companion plants with different moisture needs grouped together
Solutions:
- Ensure even flow rates in NFT channels or towers
- Reorganize plants so those with similar water demands are grouped
- Consider supplemental misting or wicking systems for hard-to-reach tower zones
Problem 5: Nutrient Deficiencies Showing Despite Balanced Feed
Symptoms:
- Yellowing between leaf veins (iron or magnesium deficiency)
- Curling, tip burn, or leaf drop on certain plants
Likely Causes:
- Certain plants are outcompeting others for micronutrients
- Your companion mix includes multiple heavy feeders in one bed
Solutions:
- Rotate crops seasonally to prevent long-term depletion
- Supplement specific micronutrients (e.g., chelated iron) based on test results
- Introduce cover crops or light feeders between harvest cycles
Final Tips for Long-Term Success
- Test and observe:Aquaponics systems are living ecosystems. What works in one setup might not in another. Trial small combinations before scaling up.
- Start small:Begin with tried-and-true companions like lettuce + basil or tomatoes + marigolds, then branch out.
- Track your results: Keep a log of which combinations thrive, which ones underperform, and any pests or issues that emerge.
- Keep things balanced:Think in terms of the whole system, plant health, fish wellbeing, and water chemistry are always connected.
Conclusion
Companion planting in aquaponics is more than just placing friendly plants together, it’s about building a resilient, efficient, and productive ecosystem. By understanding how plants interact through nutrients, root zones, pests, and physical space, you can dramatically improve your yields while reducing problems like algae blooms, pest outbreaks, and uneven growth.
Want to take your knowledge even further?
We highly recommend the Aquaponic Gardening course by Sylvia Bernstein, it’s a comprehensive, beginner-friendly video guide from one of the pioneers of modern aquaponics. You’ll learn how to design, build, and manage your system the smart way and get insights that even seasoned growers will find useful.
👉 Click here to enroll in the course now and start growing healthier plants and happier fish, faster.
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