The Aquaponic Tomatoes Growing Guide: System, Steps, Tips

Tomatoes are one of the most popular vegetables when it comes to aquaponics. But how are tomatoes grown in aquaponics systems, which steps are essential, and what else should be considered?

The rest of this article will discuss the topics essential to growing aquaponic tomatoes:

  • Can you grow tomatoes with aquaponics?
  • How tomatoes are grown in aquaponics
  • How long does it take to grow tomatoes aquaponically?
  • Expected yield
  • Are aquaponic tomatoes organic?
  • How do they taste?
  • Ideal growing conditions for tomatoes
  • The best growing system
  • The best grow media
  • Tomato variants to grow aquaponically
  • Downsides of growing tomatoes aquaponically
  • Steps to consider
  • Potential problems

Can You Grow Tomatoes With Aquaponics?

Yes, aquaponic tomatoes grow excellently and provide high yields. Tomatoes like warm temperatures and high nutrient levels and can thrive solely water-based. This makes tomatoes a brilliant fit for aquaponics systems within controlled environments.

How Tomatoes Are Grown in Aquaponics

Aquaponics is a closed-loop growing system. The waste generated by fish is pumped through a mechanical filter into grow beds.

Nitrifying bacteria on the grow media convert the fish waste into nutrients. Plants utilize water-dissolved nutrients for their growth. The purified water is then directed back into the fish tank.

In more detail, water is pumped from a sump tank into a fish loop and a grow bed loop. Following the fish loop, the water flowing into the fish tank displaces the solid-containing water pushed through the solids lifting outlet (SLO) base into the radial flow filter.

In the radial flow filter, incoming water is redirected through a stilling well, slowing down the water flow and allowing the majority of the solids to settle at the base of the filter. The clean water then exits the radial flow filter through the outlet into the sump tank.

Water is pumped constantly from the sump tank into the media beds for the grow bed loop. The beds are flooded and drained through a bell siphon mechanism once a certain water level is reached.

Nitrifying bacteria that sit on the grow media convert the ammonia to nitrates that the tomato plants then take up and use for their growth. In addition, through the water suction, the media bed and the roots of the tomato plants are supplied with air.

How Long Does It Take?

The time to grow aquaponic tomatoes depends on whether you start your plants from seed or seedling. The tomato seeds will germinate after about 6 to 8 days and grow to harvest in 90 days. Tomatoes can be harvested for up to 90 days.

Expected Yield

Aquaponic tomatoes have higher yields compared to conventional farming.

As aquaponic systems are predominantly located in greenhouses, growers can take advantage of a controlled environment in several ways:

  • Aquaponic tomatoes can be grown and harvested all year long.
  • Vertical tomato farming allows for the maximization of available space.
  • Tomato plants are continuously supplied with nutrient-rich water and do not have water stress.
  • Ideal growing temperatures and humidity levels lead to faster growth.
  • A closed and controlled environment lowers the risk of contamination or pest infestation.

The controlled growing conditions for aquaponic tomatoes translate into the following expected yields that, from my personal experience, are a good display of what to expect:

  • Growing period (start from seedlings): 90 days
  • Harvesting period: 60 to 90 days
  • Replacement of tomato plant: 2 times per year
  • Tomato yield per plant (depending on variety): 9 to 18 lbs (4 to 8 kgs)
  • Number of tomatoes per plant (depending on variety): 35 to 45 tomatoes
  • Tomato yield per year per growing spot: 18 to 36 lbs (8 to 16 kgs)
  • Number of tomatoes per year per growing spot: 70 to 90 tomatoes
  • Plus, any harvested fish from within the fish tank

Essentially, you can expect to grow two tomato plants per year on one spot with a total harvesting period of 180 days and 9 to 18 lbs (4 to 8 kgs) tomato yield.

It is important to note that the roots of the tomato plants bulk up and can impede the flow of water in the grow beds. This is why it is wise to pull out the plant, including its roots, clean off the grow media of any remainders, and put in a new plant semi-annually.

Are Aquaponic Tomatoes Organic?

Tomatoes that are grown aquaponically can be sold as locally-grown and pesticide-free. Depending on your state or country legislation and individual certification, they can also be marketed as organic, implying higher perceived quality and thus higher prices.

How Do They Taste?

Aquaponic tomatoes taste like pure tomatoes and do not taste watery. Their flavor is comparable to organic tomatoes from the farmers’ market. Moreover, aquaponic tomatoes are as fresh as possible since they are harvested on the spot, do not travel hundreds of miles, and are not stored for a couple of days.

Ideal Growing Conditions for Tomatoes

Tomatoes flourish in warm conditions. As a rule of thumb, a temperature between 65 to 80 °F (18.5 to 26.5 °C) is ideal for tomatoes to grow well. Temperatures below or above lead to reduced growth, lower yields, and reduced color setting. If you use grow lights, consider aligning these with the day/night temperature differential.

Aquaponic tomatoes grow best in more acidic conditions water with a pH of 6.0 to 6.5. pH levels above or below can lead to low nutrient uptake, leading to deficiencies.

Tomatoes require comparably high nutrition levels, especially through the fruiting phase. If the tomato plants show deficiencies, nutrition levels can be raised in the short term by adding seaweed-based and fish-safe nutrients.

Media Beds Provide the Best Yield

Tomatoes can be grown in three different aquaponic systems:

  • Floating rafts/Deep water culture (DWC)
  • Dutch buckets
  • Media beds

The best growing system for aquaponic tomatoes is media beds, as it provides the best yield per tomato plant. In direct comparison to floating rafts and Dutch buckets (same tomato variety, closed-loop system, and location), tomato plants grown in media beds have 30% to 40% more yield.

A media bed is essentially a tub filled with grow media. It is continuously flooded and drained with pre-filtered fish tank water through a bell siphon mechanism.

It provides extra air to the roots of the tomato objections every time the grow bed drains. Also, the grow media allow bacteria to settle, which converts the media beds into biofilters, positively impacting the number of fish supported by the aquaponics system.

Grow Media

Depending on personal preference and budget, the following grow media are well suited to grow tomatoes in aquaponic systems:

  • Clay pebbles/hydroton/Lightweight extended clay aggregate (LECA)
  • Expanded shale
  • River gravel
  • Other gravels such as crushed basalt

Any grow media should be 0.5 to 0.75 inches (1.3-1.9 cm) in size. Smaller-sized media will get too compact and condense the system and the roots of the plants. Bigger-sized media will leave too big air gaps that will negatively affect the growth of the tomato plants.

It is also essential to ensure that the grow media do not break down over time and is limestone-free. If the medium contains limestone, the pH level of the water will rise, and the water chemistry will change constantly.

If you decide to go with any gravel, an excellent test to make sure that the medium is limestone-free is to put one handful of the material into a small cup and fill it up with white vinegar. If no bubbles (no carbon dioxide) are released, it is limestone-free and thus safe to use in a grow bed.

Also, you want to put another handful of the grow media in distilled water for a few days. If the pH rises above the neutral 7.0, the media will cause a problem to the aquaponic system, and it will be better not to use it for your aquaponic tomato beds.

I prefer clay pebbles in media beds, as I do not want to worry about pH issues. Bacteria can settle on the porous surface of the pebbles. Moreover, the pebbles retain and release water, and are pleasant to touch.

However, no matter which material you use, rinse it thoroughly before adding it to the grow bed. This way, any dust, and fine particles stay out of the system.

Tomato Variants to Grow Aquaponically

Several tomato varieties can be grown in aquaponics systems:

  • Black plum
  • Beefsteak
  • Cherry
  • Plum
  • Heirloom

While all of the above tomato varieties grow well aquaponically, my favorite is Heirloom, as the tomatoes are different from the supermarket’s uniform types. Cherry tomatoes grow well in small aquaponic systems as they require lower nutrient levels.

Downsides of Growing Tomatoes Aquaponically

While aquaponic tomatoes are very popular and provide high yields, some downsides need to be mentioned.

Tomatoes are nutrient-demanding. As each aquaponic system has a given size and nutrient level, the number of tomato plants should be well balanced with their nutrient needs. Consider planting other less nutrient-demanding plants such as lettuce, kale, watercress, or basil to avoid overwhelming your aquaponic system.

Also, compared to other plants, tomatoes need a lot of space to flourish. You want to make sure that the tomato plants are not blocking the sunlight for other plants. Clever staking can improve light exposure.

Steps to Consider

For the following steps, I assume that you have already constructed the basis of the aquaponics system, and the water is cycling through the fish tank, radial flow filter, and sump tank, and the air pump is running.

Every aquaponics system has its characteristics and needs to be dialed in individually:

Starting Your Aquaponics System

  • Rinse the clay pebbles thoroughly and fill them into the media bed. Ensure that the pebbles overtop the maximum water level that triggers the bell siphon to drain by a little. I like the clay pebbles at about three-quarters or four-fifths of the media bed’s edge.
  • Check the water inflow into the grow bed and make sure that it floods and drains about every one to two hours.
  • The clay might be floating at this stage. Give it a couple of days to soak up the water and settle.
  • For starting the nitrogen cycle in the system, add an ammonia source and old fish feed to the fish tank and let it cycle for a few days. This will make nitrifying bacteria colonize the grow beds and thus increase nutrition levels.
  • Use a test kit for checking the nutrition levels in the water. The test kit should allow for testing pH, Ammonia, Nitrite, and Nitrate. Through regular testing, you can track the cycling of your aquaponics system.
  • Check the pH level. Make sure that it is between 6.0 and 6.5. If the pH is above 6.5, carefully apply fish-safe pH lowering solution (below 6.0 fish-safe pH raising solution) and let it run a couple of cycles through the entire system. Measure again and repeat if necessary.
  • Once your aquaponic system cycles properly, place the fish carefully into the tank. Make sure that the fish can acclimate to the water in the tank. For example, put the fish in their retaining plastic bag into the new tank and wait until the water temperature is adapted.
  • As you have a brand new system, the nitrifying cycle still is developing and nutrition levels are low. This is why you should only plant parts of the grow bed.
  • For adding tomatoes into the new system, only plant one tomato plant in the grow bed and closely monitor the development of the nitrate level with the testing kit. You can add seaweed-based fertilizer to increase nutrient levels and support plant growth. Add more tomato plants over time and consider planting less nutrient-demanding plants such as lettuce.

Starting the Tomato Plants from Seedlings or Seed

You can either start the tomato plants in the grow bed from seedlings or seeds:


If your tomato seedlings are grown in soil, give the roots a good rinse so that the earth is well removed. You want to handle the seedlings carefully as the roots are very vulnerable.

You can stick a piece of pipe into the grow bed and dig a little hole. Place the plant about 2 to 3 inches (5.08-7.62 cm) deep into the hole, pull out the pipe, and backfill any unevenness with surrounding clay pebbles.


If you want to start the tomato plants from seed, you need to consider that tomato seeds are tiny. Sprinkling these directly into the clay pebbles may work but is not ideal as they can get washed away and may end up in the system.

A better method is to use peat pellets. Peat pellets are dehydrated peat wrapped in a non-woven, biodegradable fabric.

Put the peat pellet into warm water to make the pellet swell. Once they are swollen and cooled off, pull back the top netting slightly and put in the tomato seeds.

Put the planted peat pellets into the clay pebble media until it just hits the maximum water level. The tomato seeds will germinate after about 6 to 8 days.

Another option is to use net cups filled with rock wool or perlite, also used in hydroponics.

Put the tomato plant or the seed in the media in the net cup. Then, put the net cup into the clay pebble media so that the bottom hits the maximum water level.

I like to use the peat pellets more than the net cups in clay pebble media because the net cups can break from the root growth. Nonetheless, net cups are perfect for deep water culture or NFTs.

Fish Breeds that Match Tomato-Favored Conditions

The fish breed in your aquaponic system should fit the tomato-favored temperature conditions between 65 and 80°F (18.5-26.5 °C). Also, it is essential to consider the legalities and whether it is allowed to keep the individual fish variety in your state or country.

Fish that can live in tomato-holding aquaponic systems are:

  • Tilapia (Oreochromis niloticus): 70 to 85 °F (21 to 29°C)
  • Silver perch (Bidyanus bidyanus): 73 to 83 °F (23 to 28°C)
  • Jade perch (Scortum barcoo):  75 to 80 °F (24 to 27°C)
  • Barramundi/Asian Sea Bass (Lates calcarifer): 77 to 86 °F (25 to 30°C)
  • Goldfish (Carassius auratus): 68 to 74 °F (20 to 24°C)
  • Koi (Cyprinus rubrofuscus): 65 and 75 °F (18 to 24°C)

I recommend calling a local fish hatchery and asking what fish they are offering, discussing your aquaponic plans, and hearing if they have any advice for you. You can also ask for the feeding rate and the best fish feed for your new fish. They can give you insight into how to place the fingerlings in your fish tank and the time it takes to grow them to the harvest.

Goldfish are an excellent alternative for beginners to table fish as they are pretty hardy regarding temperature and water conditions. Also, stacking requirements are much easier to handle than for larger breeds.

Determining the Scale

For providing you with an insight on how to balance your tomato-holding aquaponics system, I am assuming that you start with an IBC-sized fish tank.

A good starting point for determining the scale of your aquaponics system is the fish tank, as its size determines how many fish you can stock at maximum. Starting with a 275-gallon (1040 liters) IBC container would give you the number of fish that theoretically can live in the system and the necessary size of the grow beds.

For the maximum number of fish in the fish tank, you can apply the rule of thumb stating that one inch (2.54 cm) of fish needs one gallon (3.8 l) of water, with the first fish requiring the double amount.

If we decided to use goldfish that can grow to about 6 inches (15 cm) and 0.5 lbs (0.2 kg), we could keep 45 goldfish.

As the grow beds act as biofilters, their size determines the system’s purifying capacity and the maximum fish stocking. As a rule of thumb, a 40 x 48 x 16 inch (100 x 120 x 25 cm) grow bed has the bio-filtering ability to support 12 lbs (5.5 kgs) of fish. Our 45 goldfish would need a biofilter capacity of two grow beds with a size of 40 x 48 x 16 inches (100 x 120 x 25 centimeters) each.

For the size of the sump tank, consider that the sump tank should still hold water when the two grow beds are filled up. As a rule of thumb, the water in the media beds should account for 60% of the total water in the media beds and the sump tank.

As we have two media beds filled at a maximum of 160 gallons (600 liters), our sump tank should have a capacity of 264 gallons (1000 liters), meaning that we should add another IBC-sized tank. As you may fill the media beds only up to about three-quarters or four-fifths with water, the sump tank can be smaller, of course.

For the radial flow filter, a rain drum with a 53 gallon-capacity (200 liters) will work fine for an aquaponic system of this size.

Maintaining the Balance in the System

Tomatoes are nutrient-demanding and need space to flourish. As an aquaponic system has a given nutrient level, dialing in the number of tomato plants is essential.

Take a look at some space and caring factors of tomato plants:

  • Tomatoes should be spaced 12 inches (30 cm) from each other without offset
  • Tomatoes grow to a height between 2 and 6 feet (0.61-1.83 meters).
  • Tomatoes need a support structure
  • All tomatoes must be staked or trellised to maximize yield
  • Leaves on the bottom foot of the stem should be removed

Considering sufficient spacing, two 40 x 48 x 16 inch (100 x 120 x 25 cm) grow beds could theoretically hold 12 tomato plants (6 each). However, having this many tomato plants in the system would probably lead to nutrient deficiencies, especially at the beginning of your aquaponic system.

This is why I would start with one tomato plant in each of the two grow beds and closely monitor the nitrate level development with a testing kit. If there is enough headroom, you can gradually add more tomato plants to the aquaponic system.

If the nutrient levels do not increase over time with the age of your system, you can plant lettuce into the remaining grow bed spots, which requires a fraction of the nutrients compared to tomatoes.

Water Flow Rates and Flood and Drain Cycles

Water volume flowing into the fish tank per hour should be at a minimum equivalent to the size of the fish tank. I like to run twice the volume of the fish tank per hour.

The grow beds should be flooded and drained at a maximum of once per hour. So if you have a grow bed with a volume of 80 gallons (300 liters), the water flow should be at a maximum of 80 gallons (300 liters) per hour.

A slower water flow is good as tomato plants within the grow beds have retention times between one to four hours. I like the tomato beds to flood and drain about every one to two hours.

Accordingly, the pump in the swamp tank should be capable of processing 420 to 550 gallons (1600 to 2100 liters) per hour. Keeping the pump a little over-dimensioned allows enough wiggle room for the water being pumped into the fish tank and the grow beds and any water-friction issues occurring in the piping.

The same goes for the air pump. The air volume being pumped by the air line into the fish tank should be at least the size of the fish tank per hour to keep the fish happy. A 1000-gallon (4000 liters) per hour air compressor will be fine.

Of course, this is just a simple example to give you an orientation as your aquaponic setup will differ.

Potential Problems

While the aquaponic environment can be better controlled than traditional growing methods, aquaponic tomatoes are still susceptible to diseases and physiological disorders.

Some of the leading problems for aquaponic tomatoes are:

  • Insufficient nutrients
  • Water and oxygen
  • Gray mold
  • Powdery mildew
  • Root rot
  • Wilt diseases

Insufficient Nutrients

Nutrient levels in aquaponics depend on the number of fish, the type and size of filters, and the grow beds’ size. As tomatoes are nutrient-demanding, any insufficiencies will diminish plant and tomato growth.

If your aquaponic tomatoes suffer from nutrient insufficiencies, you can either reduce the number of tomato plants or carefully add fish-safe, seaweed-based fertilizer.

Also, you can think about adding media beds that act as biofilters, adding more filter capacity, and eventually augmenting the number of fish in your aquaponics system, ultimately increasing the nutrient level.

Water Flow and Oxygen

The right amount of water flowing into the grow beds and the amount of oxygen in the water is essential for keeping the aquaponic tomato plants healthy.

A flood and drain cycle of every second hour for the grow beds is a good starting point. For the air, at least the volume of the size of the sump tank should be fed into the sump tank per hour.

Consider adjusting the water and the oxygen flow to the day/night differential.

Gray Mold

Gray mold is caused by a fungus that can infect plant stems, leaves, and flowers. It is recognizable as gray mold that covers the flowers and the tomatoes. As gray mold occurs when there is moisture on the plant, it is a greenhouse-typical infection. It is visible on the flowers and the tomatoes.

Keeping your greenhouse well-ventilated, keeping down humidity, and keeping your gardening tools sanitized diminishes the occurrence of gray mold.

Powdery Mildew

Powdery mildew is another fungus that can infect tomatoes. The spores that are carried away in windy conditions through the air make the surface of the leaves look white. Infections mainly occur in areas near farms and fields.

Exposure risk can be reduced by ventilating your greenhouse and keeping down humidity. Also, your gardening tools should be sanitized. Be careful with fungicides or sprays, as they can get into the aquaponic cycle and harm your fish.

Root Rot

Root rot is a common problem in aquaponics and hydroponics. It may be caused by water molds if the roots are too moist and overwatered. Root rot often occurs if water cycles are too slow, if there is not enough oxygen in the water, if the roots of the tomato plants bulk up, and if the plants are placed too close to each other.

Wilt Diseases

Verticillium wilt and Fusarium wilt are frequent for aquaponic tomatoes. The fungus spreads through the water and makes the leaves of the plants yellow and wilt.

Once in the aquaponics system is a lengthy process.

First, you want to remove the infected plants and clean out the grow beds. Make sure to remove the water and give it a rinse. Then scrub down the grow beds and the pipings. You can reconnect the parts to the water cycle after leaving the corresponding parts dry for a couple of days and, at best, in warm sunlight and fresh air.

The best way to prevent your tomato plants from being infected is to regularly sanitize the grow beds, pipes, and tubs.

The Takeaway

Tomatoes grow excellently in aquaponics and provide high yields. Once the aquaponic system is set up and balanced, the growth process is fun to watch with little monitoring and caring necessary.

Juicy aquaponic tomatoes grown in your greenhouse or backyard are a delicious and rewarding experience, freeing up cash or bringing in an extra source of income if you sell them at your local farmers’ market.

This growing guide gives you an excellent introduction to growing tomatoes aquaponically. Of course, there are more nuances to aquaponics that you will get a feel for over time.

Dr. Moritz Picot

Dr. Moritz Picot is a horticulture enthusiast and the founder of, where he serves as the lead content writer. He established the website in 2022 as a valuable resource for both gardening aficionados and beginners, compiling all the gardening tips he has accumulated over the past 25 years. Alex has a passion for nurturing plants, transforming backyards into inviting spaces, and sharing his knowledge with the world.

Recent Posts