Fish Stress in Aquaponics










Aquaponic systems run pretty well for the most part, with minimal supervision needed once all the plumbing is connected and the fish are happy and the seedlings are all planted out. As a food production system, they work exceptionally well. Occasionally however things can go wrong leading to sudden fish deaths. Yesterday the fish looked fine. Today we see a dead fish and tomorrow – another. Whats going on? Is there any one simple answer to their sudden demise? Maybe not one, but a combination of factors.

One of the main killers is fish stress.

Small amounts of stress can be harmless and even beneficial for fish, but if some of the following conditions arise in your system they could jeopardize the safety of your fish. Lets take a quick tour of some of the warning signs that when mixed together with a few of the other signals can spell disaster for your fish.


Poor water quality:

Good filtration will eliminate poor water quality. Small pumps and inadequate filtration through the  the grow-bed or external bio-filter will result in water clarity issues especially if the fish load is increased. Water changes may become necessary if the levels of water impurities rise too high and your water become a cloudy or a murky colour with a frothy substance on the surface usually created by overfeeding. Stop feeding the fish and do a partial water change. Smell the water for off flavors. Bad smells means trouble in Aquaponics so you better act fast. Remove uneaten food from the bottom of the tank as it will start to decompose and result in a build up of ammonia in the system.

Water temperature:

Different species of fish require slightly different water temperatures and conditions. Try and keep large fluctuations of water temperature moderated by either having some thermal mass such as a concrete slab or even some shade cloth cover above your aquaponics fish tank to prevent sudden temperatures shifts from occurring throughout the year. A larger volume of water of 1,000 litres and more will offer stability and moderate sudden temperature swings in your system.

Water changes:

Every time you do a large water change in you tank, you are adding to the fish stress. Especially if there is a sudden pH swing because your source water is different from your main fish tank water.  A self regulation ball valve that tops water into your fish tank as the water level drops due to evaporation/transpiration is a gentle way to keep the water in your fish tanks constantly replenished.


Fish do not enjoy traveling. Transporting  large numbers of fish can have a drastic effect on their slime coat, leading to weakening their immune system. When introducing new fish into your tank, take special care to acclimatize them to the water temperature and also the pH conditions gradually with minimal disruption to their daily routine.

Handling Fish:

Limit the stress on fish by resisting the desire to net your fish regularly and show them off to your friends. Leave the fish undisturbed and allow them to feel safe at the back of the tank.Don’t handle them anymore than absolutely necessary. Use the proper weave of net to prevent your fish from being snared and gilled. Net them only when you plan to harvest and eat them.

High Ammonia

High Ammonia levels are toxic to fish. If your system is new or not fully cycled, or the fish are overfed, sudden spikes in the Ammonia levels, especially when temperature conditions are warmer than normal, can kill fish very quickly. Read this other post about water temperature, pH and Ammonia levels. Test for Ammonia regularly if your system is new or you have overfed your fish. Fish are not like dogs and cats and can go for a number of days without food to survive.

High Nitrate

Although high Nitrate levels wont kill your fish, they will feel the impact of nitrates by the time the levels reach 100 ppm, particularly if levels remain there for some time. The resulting stress leaves the fish more susceptible to disease. A high Nitrate reading should alert you to either reduce the number of fish in your tank, or add more grow-beds and increase your number of plants to suck up the excess nutrients. An aquaponics system in balance has low to no Nitrate readings and is a picture of  lush vegetation. Your plant growth will give you a good indication of the health of the system. Algae growth in your tank is also a good indicator of high Nitrates in your system. Nitrate levels as low as 10 ppm will promote algae growth. Make sure you keep harvesting your plants and planting our seedlings to keep the system always in balance.

Improper pH level

An Aquaponics System is a trade off between the ideal pH range that the fish prefer (7-7.5) and the ideal range that the plants prefer (mid 6’s). Keep your pH monitored regularly to ensure your system is running at peak capacity. A pH around the mid 6.4 to 7 is the ideal range to keep both fish and plants happy. Outside these parameters the fish health will begin to strain a little and the plants ability to take up the range of nutrients will be severely diminished.

Salt baths alleviate stress

Salt baths are commonly used in aquaponics as a tonic to shock and kill parasites that may be lurking on  fish. Salt is also also used to de-stress  fish used in aquaponics. When fish are stressed they react by excreting minerals into the water. If this condition persists for an extended period of time, the salt loss can be fatal for the fish. The survival chances of fish can be significantly increased by adding a little salt to their water. Since mineral excretion is directly linked to the concentration of salt in the water, increasing the water salinity reduces salt excretion and stress for the fish. The normal recommended salinity level to dose the fish is in the range of 0.5-3 ppt. Be aware that adding a high dosage of salt into your system is a double edged sword as some plants like strawberries will not tolerate salt levels beyond 3 ppt. Do not dose higher than recommended as this will also kill both your fish and plants.

Fish 02 Chart

Low oxygen levels

Low oxygen levels in the fish tank will result in fish attempting to ‘breathe’ faster than normal resulting in chronic stress and eventual fish deaths. Different fish require different amounts of dissolved oxygen in the water. Trout for instance require dissolved oxygen at 6ppm. Whilst other more ‘hardy’ fish require less. Make sure you have adequate aeration going into your tank at all times especially during warmer summer months as dissolved oxygen is more difficult to saturate the water as the water temperature rises.

Harassment from other fish

Although some mixing of fish species will work out okay, be careful about mixing your fish with unsuitable fish species that are predatory in nature and territorial to the other fish. In general it is preferable to stock your tank in aquaponics with the one species of fish for maximum ease of management. Feeding the right protein diet for your fish is also an important factor that can be monitored carefully if only the one species is stocked in your tank.

Overstocking of tank

Overstocking the tank with fish is just asking for trouble resulting in increasing poor water quality as the fish mature and the greater oxygen demand will place a limit to your system’s capacity to meet that need.  We had 50 Jade Perch in a 1000 litre tank that grew fine while they were young but as the fish matured, the increased fish size began to put a limit on our system’s ability to handle the increased load. We had to harvest the fish. Failure to keep the system in balance will result in problems. It only required a pump failure or the aerator to malfunction and the whole system can come crashing down. As one Aquaponics veteran remarked recently, “Aquaponics should be a pleasure – not a chore!” Keep your system balanced and resist the urge to overstock your fish tank and all will be well.

Disturbance of the tank

Jade Perch in our aquaponics system would sometimes leap and hit the sides of the tank at night when the main light above their tank was suddenly turned on. Keep the disturbance level to the minimum. This means keeping the fish tank covered with a heavy timber lid to minimize direct sunlight and also keeping the fish tank protected and subdued from sudden noise or  bursts of  bright light.

Lack of enough fish to provide schooling

Fish love the company of their own species for schooling in reasonable numbers and as a safety precaution from predators. They feel happier in a larger group. Their natural instinct is to keep nice and close together. Make sure you have enough fish in your tank to make  them feel safe and comfortable.


Aquaponics is an Eco-system

Fish in a natural environment have a healthy slime coating that prevents bacterial infections and parasites from attacking them. When stressed fish are more susceptible to a weakening of their natural defenses. By recognizing some of these points in your system, you can be more alert and guard against some of the tell tale signs that are detrimental to the health of your entire aquaponics system.



Green Tree Frog

Green Tree Frog sitting on Basil Leaf in our Aquaponics System




In Murray Hallam’s Aquaponics Secrets DVD, he emphasizes the point that an Aquaponics system should be constructed in such a way to mimic or imitate a natural eco-system. Within months of running our own system as outlined by Murray, our grow-beds began to attract all sorts of small exotic creatures. Native honeybees would visit the flowering basil bushes.

Our system became the resident home for a lively Green Tree Frog, attracted by the running water, small beetles, insects and compost worms that slithered amidst the red clay balls. The frog also kept small predator bugs in check.

Fish thrive best when all their survival needs are met. Just like in a wild mountain stream somewhere in the Rocky Mountains, with fast flowing pristine water that is well oxygenated, your fish should also live in such an environment. They should be lively, alert, happy and hungry for food. Give them a home that they will enjoy and they will  respond and grow healthy, fat and ready to jump on your dinner plate.