How to Care for Fish in Aquaponics

When most people think of aquaponics, they see a picture of lush greens and vegetables growing effortlessly in water, but at the heart of every successful aquaponics system is something just as important: healthy, well-cared-for fish.

In aquaponics, fish aren't just part of the system, they power it. Their waste provides the essential nutrients that feed your plants, and in return, plants and beneficial bacteria help clean the water the fish live. This natural cycle only works when your fish are healthy, stress-free, and living in optimal conditions.

Unfortunately, many beginners focus heavily on plant growth and ignore fish care until it’s too late. Unstable water quality, poor feeding routines, and overlooked stress signals can all lead to sick or dying fish, and when your fish suffer, your plants will too.

In this blog, we will walk you through exactly how to care for fish in aquaponics, including:

• Choosing the right fish species for your system
  
• Maintaining optimal water quality (like pH, ammonia, and oxygen levels)
  
• Setting up a proper feeding schedule
  
• Identifying early signs of fish stress or illness
  
• Seasonal adjustments and routine maintenance tips
  

Whether you’re just getting started or troubleshooting an existing system, this blog will give you a complete understanding of aquaponics fish care, because when your fish thrive, your entire ecosystem thrives.

Choosing the Right Fish for Aquaponics

Selecting the right fish species is one of the most important decisions you’ll make in setting up or maintaining your aquaponics system. Your choice will influence everything from water temperature requirements to feeding schedules and system design.

1. Best Fish for Aquaponics Beginners

For those just getting started, it’s best to choose hardy fish that can tolerate a range of water conditions and are less prone to stress or disease. Here are some of the most popular and beginner-friendly species:

• Tilapia– One of the most common aquaponics fish due to their fast growth, hardiness, and adaptability. However, check your local regulations—in some regions, tilapia require permits or are restricted.
  
• Goldfish– Ideal for small systems or indoor setups. Goldfish are tough, inexpensive, and easy to feed.
  
• Koi– Koiare known for their resilience and long lifespan. Great for decorative systems or outdoor setups, though they grow large and need space.
  
• Catfish – Catfish thrive in warm water systems and grow quickly. Require more oxygen, so they’re best for more advanced systems.
  
• Trout – Trout are great for cooler climates but require precise water conditions and higher oxygen levels.
  

2. Climate & Temperature Compatibility

Each fish species has its own temperature comfort zone. For example:

• Tilapia prefer 75–86°F (24–30°C)
  
• Trout need cooler water: 50–60°F (10–16°C)
  
• Goldfish and koi can handle wider temperature ranges
  

Make sure to choose fish that match your climate or invest in heating or cooling solutions if needed.

3. Understanding Stocking Density

Stocking density refers to how many fish you can safely keep per gallon or liter of water. Overstocking leads to poor water quality, stress, and disease outbreaks. A general rule of thumb is:

• 0.5–1 lb of fish per 5–10 gallons of water, depending on your system’s filtration capacity and grow bed size
  

Always start with a lower density until your system is cycled and stable.

4. Fish Compatibility in Mixed Systems

While it’s possible to keep multiple fish species in one system, beginners should stick with a single species to simplify care. If you do want to mix, consider:

• Similar temperature and pH needs
  
• Similar growth rates and feeding habits
  
• Avoid mixing aggressive species with peaceful ones
  

5. Legal and Ethical Considerations

Some fish, like tilapia or trout, are subject to regional farming regulations. Always check:

• Local aquaculture or agriculture department guidelines
  
• Whether you need a permit to raise or transport fish
  
• Restrictions on releasing fish into local waterways
  

Tip: Before buying fish, make sure your system is fully cycled and stable. Introducing fish to a system with ammonia spikes or pH imbalances is one of the fastest ways to create stress and health problems.

Understanding Fish Needs in a Closed Aquaponics System

In a traditional pond or aquarium, fish rely on mechanical filters and water changes for a clean environment. In aquaponics, the system is self-contained, which means that your fish, plants, and bacteria  all depend on each other to survive. Because of this, understanding the unique needs of fish in a closed-loop system is essential to keeping them healthy.

The Nitrogen Cycle: The Engine of Aquaponics

At the heart of every successful aquaponics setup is the nitrogen cycle, a biological process that converts toxic fish waste into nutrients plants can use.

Here’s how it works:

1. Fish produce waste, primarily in the form of ammonia (NH₃), which is toxic at even low levels.
   
2. Beneficial bacteria (Nitrosomonas) convert ammonia into nitrites (NO₂⁻).
   
3. Another type of bacteria (Nitrobacter) then converts nitrites into nitrates (NO₃⁻), which are far less harmful to fish and highly beneficial to plants.
   

Maintaining a healthy population of these bacteria is critical. This process is known as cycling your aquaponics system, and it should be completed before you add fish. Without a cycled system, toxic ammonia levels can build up quickly, leading to stressed or dying fish.

Tip: Test your water regularly during the cycling phase. You’ll know your system is ready for fish when ammonia and nitrite levels drop to near zero and nitrates begin to rise.

Why Stability Matters

Unlike natural ecosystems, aquaponics systems don’t have outside buffers like rain, soil, or predators. This is why a small issue. such as a rise in pH or drop in oxygen can quickly spiral into a major problem.

Fish in these systems rely on you to manage:

• Water parameters (pH, ammonia, oxygen)
  
• Feeding routines
  
• Population control
  
• Stress reduction during system changes
  

Even introducing new fish too quickly can throw off your biofilter and bacteria colonies. Always quarantine new arrivals and acclimate them slowly to the water temperature and pH.

Monitoring and Maintaining Water Quality

Luckily, you don’t need to be a chemist to monitor and maintain the water qualityof your system. With a few tools and a consistent routine, you can easily monitor and maintain a balanced aquatic environment for your fish and plants.

1. Essential Water Parameters to Monitor

Here are the five most critical factors to track regularly:

1. Ammonia (NH₃)

• Ideal range:0 ppm (parts per million)
  
• Produced by fish waste and decomposing food
  
• Toxic to fish at even low levels
  
• Spike = overfeeding, poor filtration, or an uncycled system
  

2. Nitrite (NO₂⁻)

• Ideal range:0 ppm
  
• Intermediate stage in the nitrogen cycle
  
• Also toxic to fish—causes respiratory stress
  
• Indicates biofilter isn't fully mature yet
  

3. Nitrate (NO₃⁻)

• Ideal range:20–60 ppm (for plant uptake)
  
• Much less harmful to fish than ammonia or nitrites
  
• High nitrate = great plant growth, but excessive buildup can stress fish
  

4. pH

• Ideal range:6.8 to 7.2 (slightly acidic to neutral)
  
• Affects nutrient availability and bacterial efficiency
  
• pH naturally drifts downward over time in aquaponics
  
• Avoid rapid swings—adjust slowly using safe methods like potassium bicarbonate
  

5. Dissolved Oxygen (DO)

• Ideal range:5–8 mg/L
  
• Fish need oxygen-rich water to survive and grow
  
• Low oxygen = fish gasping at the surface, slowed growth, and biofilter failure
  
• Add aeration with air stones, pumps, or waterfalls
  

2. Water Testing Tools You’ll Need

To keep your system in balance, use:

• Freshwater Master Test Kit (API or similar): tests ammonia, nitrite, nitrate, and pH
  
• Digital pH meteror test strips
  
• Dissolved oxygen meter (optional, but helpful)
  
• Thermometer: water temperature affects all chemical processes
  

Tip:Test water daily when first cycling your system. After stabilization, test 1–2 times per week.

What to Do When Readings Are Off

Here’s a quick response guide for imbalances:

Feeding Your Aquaponics Fish

Proper feeding is more than just keeping your fish alive as it directly impacts water quality, fish growth, and the overall health of your aquaponics ecosystem. Overfeeding can pollute your water, while underfeeding stresses your fish and slows growth.

1. How Often and How Much to Feed

• Feed 1–2 times daily, offering only what your fish can consume in about 5 minutes.
  
• Younger fish or fingerlings usually need more frequent feeding (up to 3 times per day).
  
• Observe fish behavior during feeding: if food is left uneaten after 5 minutes, reduce the amount next time.
  
• Avoid feeding right before lights off or when fish are less active, to minimize waste.
  

2. Choosing the Best Food for Aquaponics Fish

Your fish’s diet depends on their species, but here are some common options:

• Commercial pellets: Most common, formulated to provide balanced nutrition.
  
• Look for floating pellets to monitor feeding easily.
  
• Choose species-specific pellets (tilapia, koi, catfish formulas).
  
• Live or frozen foods: Like brine shrimp or bloodworms, great for variety and added protein.
  
• Homemade or organic fish food: Some aquaponic growers blend grains, vegetables, and supplements for a natural diet.
  
• Avoid over-reliance on flakes or bread, which can pollute water quickly.
  

3. Signs of Overfeeding and Underfeeding

• Overfeeding indicators:
• Cloudy or smelly water from uneaten food decay
• Excessive algae growth due to nutrient spikes
  
• Fish waste buildup stressing filtration
  
  
• Underfeeding indicators:
  
  
• Fish become thin or lethargic
  
• Slow growth rates
  
• Increased aggression or competition at feeding time
  

4. Managing Fish Food Waste and Water Quality

Fish foodthat isn’t eaten quickly breaks down into ammonia, which raises toxic levels and disrupts the nitrogen cycle.

• Use feeding trays or barriers in larger tanks to reduce food waste.
  
• Remove visible uneaten food promptly.
  
• Maintain consistent feeding routines to support bacterial balance.
  
• If water quality issues persist, consider reducing feeding amounts or frequency temporarily.
  

Recognizing Fish Stress and Preventing Disease

Fish don’t always show obvious symptoms until a problem becomes severe, so learning to recognize subtle changes is crucial for timely intervention.

1. Common Signs of Fish Stress

Stress weakens fish immune systems and can lead to illness. Watch for:

• Erratic swimming or lethargy
  
• Gasping at the water surface (sign of low oxygen)
  
• Clamped fins (fins held close to the body)
  
• Loss of appetite
  
• Visible spots, lesions, or discoloration
  
• Excessive scratching or rubbing against surfaces
  

2. Common Diseases in Aquaponics Fish

While a balanced system reduces disease risk, these are the most common issues:

• Ich (White Spot Disease):White spots on body and fins, caused by parasites.
  
• Fin Rot:Fins appear ragged or disintegrated, often from bacterial infection.
  
• Fungal Infections: Cotton-like growths on skin or gills.
  
• Dropsy:Swelling of the body due to internal infection or organ failure.
  
• Ammonia Poisoning: Red or inflamed gills, lethargy, and gasping.
  

3. Preventing Disease Naturally

• Maintain optimal water quality (regular testing and balancing).
  
• Avoid overcrowding to reduce stress and disease transmission.
  
• Quarantine new fish for at least 2 weeks before adding them to your system.
  
• Use natural remedies where appropriate, like aquarium salt or herbal treatments.
  
• Keep your system clean by removing uneaten food and debris.
  
• Consider adding beneficial probiotics to enhance fish immunity and biofilter health.
  

4. When to Consult a Specialist

If fish show severe or persistent symptoms, consult an aquaculture veterinarian or local fish health expert. Early professional intervention can save your fish and protect your aquaponics investment.

Seasonal Care and System Maintenance

Aquaponics is a living ecosystem that changes with the seasons. Adjusting your fish care routine and system maintenance accordingly ensures your fish stay healthy and productive all year long.

1. Spring and Summer: Growth and Activity

• Fish metabolism and appetite increase in warmer water.
  
• Increase feeding frequency slightly but avoid overfeeding.
  
• Monitor oxygen levels closely, as warm water holds less oxygen.
  
• Check and clean filters and pumps more frequently due to increased bio-load.
  
• Watch for algae growth and control with shading or aquatic plants.
  

2. Fall and Winter: Slower Metabolism and Temperature Management

• Fish become less active and eat less as water cools.
  
• Reduce feeding frequency and portion sizes to prevent food buildup.
  
• Use heaters or insulation to keep water temperature stable, especially for warm-water fish like tilapia.
  
• Monitor temperature fluctuations closely because sudden drops can stress fish.
  
• Ensure aeration remains strong, as cold water holds more oxygen but fish consume it differently.
  

3. Routine Maintenance Tips

• Test water parameters regularly (at least weekly) regardless of season.
  
• Clean mechanical filters and remove sludge buildup.
  
• Inspect pumps, air stones, and plumbing for blockages or wear.
  
• Remove dead plant material and uneaten fish food daily.
  
• Perform partial water changes if nitrate levels get too high.
  

4. Preparing for Extreme Weather

• Have backup power or aeration systems for heatwaves or cold snaps.
  
• Protect outdoor tanks from freezing temperatures with covers or heat tape.
  
• Consider temporary indoor relocation for sensitive fish species during harsh weather.
  

Seasonal Adjustments in Fish Care

As the seasons change, so do the needs of your aquaponics fish. Understanding how seasonal factors affect fish behavior, metabolism, and health helps you tailor your care routine to keep your system balanced and your fish thriving.

1. Spring: Increasing Activity and Growth

• Water temperatures begin to rise, boosting fish metabolism.
  
• Increase feeding gradually to match their growing appetite.
  
• Begin regular health checks for any signs of stress after winter dormancy.
  
• Monitor water parameters closely as increased feeding and warmer temperatures can shift nitrogen levels.
  

2. Summer: Peak Growth and Oxygen Management

• Fish reach peak activity; feeding 2–3 times daily may be necessary.
  
• Oxygen levels can drop in warmer water, so ensure good aeration and circulation.
  
• Increase system monitoring frequency, especially for ammonia and nitrate spikes.
  
• Shade tanks or use floating plants to reduce water temperature and control algae.
  

3. Fall: Slowing Metabolism and Preparing for Cooler Months

• Gradually reduce feeding frequency as water cools.
  
• Observe fish for reduced activity and appetite.
  
• Maintain steady water temperature as fluctuations can stress fish.
  
• Prepare system for winter by checking heaters and insulation if needed.
  

4. Winter: Conservation and Care

• Fish metabolism slows significantly; feed sparingly or even pause feeding for some species.
  
• Use heaters or insulation to prevent temperature drops below fish tolerance.
  
• Minimize disturbances as fish are more sensitive to stress in cold conditions.
  
• Keep aeration running steadily to maintain oxygen, as cold water holds more oxygen but fish consume less.
  

Additional Seasonal Care Tips

• Adjust stocking density if possible, reduce numbers during colder months to lessen bio-load.
  
• Quarantine any new fish thoroughly, as fish are more vulnerable to disease during temperature transitions.
  
• Keep a close eye on fish behavior such as changes in swimming patterns or appetite can indicate stress from seasonal shifts.
  

Troubleshooting Common Fish Problems in Aquaponics

Even with the best care, aquaponics fish can face challenges. Knowing how to quickly identify and address common problems can save your fish and protect your entire system.

Problem 1: Ammonia or Nitrite Spikes

Symptoms:

• Fish gasping at the surface
  
• Red or inflamed gills
  
• Lethargy or erratic swimming
  

Causes:

• Overfeeding
  
• Overcrowding
  
• Uncycled or failing biofilter
  

Solutions:

• Immediately reduce or stop feeding
  
• Perform a partial water change (10–20%) to dilute toxins
  
• Add beneficial nitrifying bacteria supplements
  
• Check and clean biofilters and pumps
  
• Reduce fish stocking density if necessary
  

Problem 2: Low Dissolved Oxygen

Symptoms:

• Fish surface gulping
  
• Slow movements or resting at the tank bottom
  

Causes:

• Insufficient aeration
  
• High water temperature
  
• Overcrowding
  

Solutions:

• Increase aeration with air stones, pumps, or waterfalls
  
• Add shading or floating plants to cool water
  
• Reduce fish population or temporarily stop feeding
  

Problem 3: Disease Outbreaks

Symptoms:

• Visible spots, ulcers, or fungal growth
  
• Loss of appetite and lethargy
  
• Unusual swimming or scratching behavior
  

Causes:

• Poor water quality
  
• Stress from sudden changes or overcrowding
  
• Introducing infected fish without quarantine
  

Solutions:

• Quarantine and treat affected fish with appropriate medications
  
• Improve water quality by testing and adjusting parameters
  
• Reduce stocking density and avoid rapid system changes
  
• Use natural remedies or probiotics to boost fish immunity
  

Problem 4: Algae Overgrowth

Symptoms:

• Green water or slimy tank surfaces
  
• Clogged filters and reduced oxygen
  

Causes:

• Excess nutrients from overfeeding or high nitrates
  
• Too much light exposure
  

Solutions:

• Reduce feeding and remove uneaten food promptly
  
• Add more plants to absorb excess nutrients
  
• Limit direct sunlight or use shade cloth
  
• Clean tanks and filters regularly
  

General Troubleshooting Tips

• Keep a log of water parameters and fish behavior to track patterns.
  
• Make changes gradually to avoid shocking fish or bacteria colonies.
  
• Always quarantine new fish and plants before adding them to the system.
  
• Maintain routine system checks to catch problems early.
  

Conclusion: Thriving Fish, Thriving System

Caring for fish in aquaponics is both an art and a science. When your fish are healthy, active, and well-fed, your entire system thrives and the plants grow stronger, water stays cleaner, and your ecosystem stays in balance.

From monitoring water quality and feeding smartly to making seasonal adjustments and troubleshooting problems, your attention to detail makes all the difference. Remember, the health of your fish isn't just about survival, it's about creating a thriving, self-sustaining environment where everything works together naturally.

Ready to Take Your Aquaponics Skills to the Next Level?

If you're serious about building a resilient and productive aquaponics system, we highly recommend enrolling in the Aquaponic Gardening course by Sylvia Bernstein on Udemy. Sylvia is one of the most trusted voices in the aquaponics world, and her step-by-step course offers in-depth guidance for both beginners and intermediate growers.

Click here to check out the course on Udemy

You’ll gain the confidence and practical knowledge to manage fish, plants, and water with expert precision, so you can grow more food with less guesswork.

Have questions about fish care or your aquaponics setup? Drop them in the comments below or reach out to us, we love helping fellow growers build better systems.