How to Plant in Aquaponics Systems

Planting in your aquaponics systems is easy! You can treat it just like any standard garden, and you can grow various plants. Growing your own food at home with aquaponics may be simple, but you need to know a few basic things before getting started. In this guide, we will walk you through the process of planting in your aquaponics system.

Getting Started

Once your system is assembled and ready, you need to start “cycling” or establishing the bacteria in your system, so your plants will grow. The cycling process happens automatically in all cases, and testing and monitoring the process is essential to ensure the bacteria is established well. The methods of cycling are:

  • Cycling with fish

Cycling with fish is the old method of cycling new aquaponics systems and can take 25-40 days. It is because the nitrifying bacteria grow relatively slowly in this method. 

Steps on Cycling with Fish
  1. Start fish cycling by adding a few fish to the fish tank. Add only a few fish because too many will cause the ammonia levels to spike and harm the fish. 
  2. Once your fish are in, feed them lightly to start producing waste and start the cycle.
  3. Monitor the ammonia, nitrite, and nitrate levels daily to ensure they do not get too high. If the ammonia level is more than 3.0 ppm, you must do a partial or complete water change to avoid an ammonia spike. Ammonia should remain below 3.0 ppm, nitrite below 1.0 ppm, and the nitrate level should increase over time.
  4. Continue monitoring ammonia, nitrite, and nitrate levels and replace the water as needed until your fish tank is fully cycled. Your aquaponics system is fully cycled when your ammonia and nitrite levels remain below 0.25 ppm.
  • Fishless Cycling

Fishless cycling has become the most popular cycling method of new aquaponics systems today. It takes a few days and offers more advantages over cycling with fish. First, the grower and the fish will endure less stress while cycling. Second, no fish are involved in the process, so you don’t need to be overly concerned when ammonia, nitrite, and pH levels go up. The sources of ammonia for fishless cycling are liquid ammonia, ammonium chloride, urine, and dead fish. 

Steps of Fishless Cycling
  1. When your aquaponics system is ready, begin by adding an ammonia solution a little at a time to the fish tank until your reading from the ammonia test is -5 ppm.
  2. Record the amount of ammonia it took to reach the -5 ppm and then add that amount daily until the nitrite appears at 0.5 ppm.
  3. Once nitrites appear, cut back the daily dose of ammonia to half of the original volume.
  4. Once nitrates appear at 5 – 10 ppm and nitrites have dropped to zero, your system is fully cycled, and you can start adding your fish.


What And When To Grow In Aquaponics

Different plants grow under other conditions. Some plants can thrive and grow in a floating raft, like lettuce and leafy greens, while root vegetables and fruiting plants grow better in media beds. 

When deciding what plants to grow in your aquaponics system, it is important to choose varieties of vegetables that will grow best in your climate. Temperature is hard to control, even if you’re growing in a greenhouse. Plants thrive better when the temperature matches their typical habitat. So grow cold-weather crops in colder months and warm-weather crops during summer. 

Succession planting allows some of your plants to mature and be harvested while the newer ones grow and come in behind. Succession planting will ensure that you always have plants taking nutrients from the water.

Important Considerations Before Planting

  • Planting Design: The layout of your grow bed will maximize your plant production in the available space. Before planting, choose wisely what plants you will grow, bearing in mind the space needed by each plant.
  • Plant Diversely: Plants are susceptible to diseases and parasites. If only one crop is grown, the chance for severe infestation is higher, which can unbalance the whole aquaponics system. That is why planting a diverse range of plants is encouraged.
  • Staggered Planting: Staggered planting is important so there can be constant harvest and replanting, which will help maintain the balance of nutrient levels in the system.
  • Maximize Your Grow Bed Space: Maximize the surface area of your grow bed and the vertical space and time. The benefit of this practice is that you can harvest the salad greens while providing more room for the eggplants to mature.

How to Germinate Seeds

All seeds need water, oxygen, and the proper temperature to germinate. Water and oxygen are taken through the seed coat when the seed is exposed to the appropriate condition. Then the embryo’s cells will enlarge, and the seed coat will break open for the root to emerge, followed by the shoot that contains leaves and stems. 

Over-watering, insufficient oxygen, planting seeds too deeply, and dry conditions can cause poor germination. Some seed coats are so hard that water and oxygen can only get through when the skin breaks down. Soaking or scratching the seeds will help break down the seed coat and allow the seed to germinate faster.

Seed Starting Techniques

Below are the three major ways of starting seeds in aquaponics.     

1. Direct Sowing

Some seeds can be sown directly in your grow beds. This method is used in a media-based system, where they grow media like pebbles or gravel to support the seed growth. 

Spread the seeds out evenly, push them down under the top dry layer of your growing media, and then wait for them to germinate naturally. This method works well for leafy greens and herbs like lettuce and chard. However, some seeds germinate better than others under these conditions, so you need to sow many seeds expecting not all of them will germinate. 

The advantage of the direct sowing method is that you need not transplant your plants to your grow bed, eliminating the possibility of damaging the plant’s roots

2. Starter Plugs

Starting seeds in a separate media plug and placing it in your grow bed is a great way to arrange your plants in your grow bed. Then carefully cover the plug with your grow media. Starter plugs are best used for harder-to-germinate seeds or need more time and care, like tomatoes, peppers, and eggplant. Once the seeds germinate to your desired size, they can be transferred into your grow bed by making a small hole and gently placing the seedling. 

The different starter plugs used by growers are rock wool and peat. Compressed peat, rock wool, and paper towels are the most common because they are inexpensive, sterile, and easy to find.

3. Cuttings and cloning

Some plants can be grown in Aquaponics by sticking cuttings directly into your grow bed. Fast-growing herbs like basil and mint will sprout from cuttings, making them a great way to plant without using seedlings. Rooting hormones that induce new roots can be used by dipping the cut end into the rooting hormone. 



Transplanting Seedlings

You can get seedlings from a store or start seeds yourself. Once your seeds sprout, good soil and strong light will help them grow. When transplanting your seedlings from the soil, fill a small container with water and gently rinse the dirt off the roots before placing the plant in the media, deep enough for the roots to touch the water. Applying rooting compounds can help because transplanting can sometimes damage the plant’s roots. 

Tips on Transplanting Seedlings

  1. If you’re planting into a new grow bed, it is advisable to plant seedlings rather than seeds. This is because seedlings will start extracting nutrients right away.
  2. Always remember that plants need plenty of space to grow to keep them from competing for nutrients, so give them enough room to grow.
  3. Always be gentle when planting your seedlings. Roots are very sensitive, and it might take a few days for a new plant to settle into its new environment. 
  4. Wash the soil out of the root system of the plants very gently because it may carry plant pathogens that can hurt your system.
  5. Structure your plantings so that large or tall plants like tomatoes are grown on the far side of the grow bed so that they will not cover or shade smaller plants. 
  6. It is recommended to plant at dusk so that young seedlings can acclimate to the new environment before the morning sun.
  7. It is best to stagger the planting to prevent harvesting the entire crop all at once. Harvesting plants all at once will decrease the nutrient levels, which might create nutritional problems and stress for the fish. Staggered planting also allows for continual harvest and transplant of crops and helps ensure constant nutrient uptake and water filtration.

Media Bed Planting Tips

  • Place seeds in separate media plugs and wait for them to grow to your desired sizes.
  • Transfer your seedlings into the grow bed by pushing aside some media to make a small hole (about 5cm) and gently placing the seedling in it, with the roots in a downward position.  
  • Carefully cover the roots with media and, if necessary, use stakes or ties to support the seedling until the roots grow out of the plug to hold it up.
  • When planting in your grow bed, plant densely, and you can plant a lot closer together than you would in soil because the plants will have as much water as they want.
  • Try to make use of areas where plant growth can expand and extend. If your grow bed is near a wall or fence, plant climbers like beans, cucumbers, or tomatoes. 

NFT Planting Tips

  • To grow plants in the grow pipes, you need to support the seedlings with a short pipe or net cup that contains 3-4 cm of growing media. 
  • It is best to fill the net cup with a mixture of media and a moisture-retaining medium like compost. The compost will help retain the moisture because the young plant roots barely touch the water flow in the grow pipe. 
  • After a week, the roots should have extended out the net cup into the grow pipe with access to the water flowing inside the pipe.
  • If necessary, wicks can be extended from the bottom of the net cup into the stream of water.

Raft Planting Tips

  • Like planting in NFT systems, Raft systems need the plants to be supported using a small net cup filled with 3-4 cm of growing media and placed into the holes in the rafts on top of the water.


An aquaponics system requires some work, and it is an ongoing project and experiment, but it is worth it. The benefits and satisfaction you get from growing and harvesting fresh, healthy food for you and your family are worth all your efforts.