How To Successfully Start Your Aquaponic Seeds

Getting started in aquaponics can be daunting. One very important step in an aquaponics system is choosing the right seeds to plant and planting them properly. Many people balk at the sheer volume of possibilities when choosing the correct plant life to complement the rest of your aquaponics system, but it doesn’t have to be so difficult.

Here’s how to successfully start your aquaponic seeds:

  1. Lay the proper groundwork.
  2. Measure the bacterial growth and nutrient level.
  3. Choose the best plants for your system.
  4. Plant the seeds using an appropriate technique.
  5. Maintain proper conditions to yield a successful harvest.

Although there’s quite a bit to consider, your aquaponic seeds should turn out fine as long as you follow the right steps with proper due diligence. This article will provide you with all the knowledge you’ll need to make your aquaponic seeds a success.

1. Lay the Proper Groundwork

Starting a successful hydroponics system within your aquaponic system requires the other areas of your operation to be running smoothly.

Getting started successfully with your plant life requires far more than just planting the seeds. You’ll also need to ensure the correct groundwork has been done before you can even think about introducing seeds to the system.

Aquaponics combines two thing: aquaculture and hydroponics. While there are some other things to consider, these two stand out as the backbone of the entire system. One cannot thrive without the other. 

For this reason, you must first consider the aquaculture part of the system that breathes life into the plant life before learning how to plant seeds or choose the right plant life for your hydroponic system.

Laying the right groundwork means your aquaculture must be done right so it can produce enough ammonia to keep your hydroponics running smoothly. Similarly, there must be enough nitrogen-converting bacteria in the water to ensure the well-being of the fish and that plants make it to adulthood.

Getting the Aquatic Life Right

Getting your aquatic life right is one of the most important for any aquaponic system that hopes to gain any degree of success. While the plant life keeps the fish going, the fish contributes directly to the productivity of the entire system. 

There is quite a lot to know here, but the two main things to get right are:

  • Stocking the right type of fish
  • Stocking the proper amount of fish

Selecting Types of Fish

The type of fish you choose depends on what you hope to achieve with your aquaponics system. The most popular choice is freshwater fish that handle stress well and grow properly under artificial conditions.

One of the most tried and tested is the Nile tilapia fish (Oreochromis niloticus). Generally speaking, tilapia is one of the hardiest species of fish to raise.

They’re strongly resistant to many of the common diseases and pathogens encountered with other species, making them a strong pick. Along with this, they’re far less fussy than most of the other potential choices, being able to withstand temperatures between 55-85 °F (12-30 °C).

Another good choice is the carp (Cyprinus carpio). The carp stands as the most popular choice for rearers in many fields. It’s the single most reared fish globally, even more than tilapia. It can withstand an even wider range of temperatures and does well in captivity.

Deciding How Many Fish to Use

Once you’ve decided on the type of fish you would like in your system, the next thing to choose is the amount of that fish to keep.

Generally, there’s an accepted consensus that you should keep as many fish as your system can handle. This line of reasoning doesn’t mean you should stuff the tubs so full of fish that they can’t breathe. Rather, find a happy medium.

A good middle ground exists between having enough fish to meet the plants’ needs but not an abundance of fish that lack enough oxygen to go around. 

Getting Your Bacterial Life Right

One of the main tenets of any aquaponic system is the nitrogen cycle. There’s a lot involved if you truly hope to understand the nitrogen cycle, how it works, and its importance to aquaponics.

While an extensive explanation would require a separate dedicated article, it’s pertinent to highlight some key points here.

Ammonia Is Key

Ammonia is a key feature of aquaponics. Ammonia is a nitrogen compound introduced to the system from fish waste, fish feed, and dead fish.

In large enough quantities, it’s toxic to the fish, so it must be managed properly to optimize your aquaculture process. The main objective is to convert toxic ammonia to nitrites which the plants use.

This point is where nitrifying bacteria come in.

Nitrifying Bacteria 

There are two major types of bacteria involved in converting ammonia to nitrites.

The first of these is nitrosomonas. Nitrosomonas converts ammonia present in the water into nitrites which are less toxic to fish. Following this, another form of bacteria (usually nitrobacter) converts the nitrites to nitrates.

Nitrates are the form that is beneficial to plant life and is the link between hydroponics and aquaculture. In essence, bacteria combine these two separate processes and make them symbiotic. As a result, establishing a proper colony is essential to any system that hopes to thrive.

The process of this is called cycling.

Cycling Your System

Cycling involves converting ammonia in the water to nitrites by promoting the growth of nitrifying bacteria. This is a critical process, and it’s important to note that cycling must be done before introducing fish into the system.

To get this process going, introduce incremental amounts of ammonia into the pond over a specific period to slowly promote the growth of nitrifying bacteria.

One major way to promote this bacterial growth is by using a biofilter. The biofilter provides the surface area, pH, dissolved oxygen levels, and other parameters required for proper bacterial growth.

On the other hand, if you use the right grow bed, a biofilter might be superfluous since there could already be enough bacterial growth. 

2. Measure the Bacterial Growth and Nutrient Level

After the cycling process has run for a few weeks in your empty hydroponics system, you can begin to measure the level of bacterial growth in the water. This will determine if it’s the right time to start your aquaponic system properly.

There are three main things to try to take note of here:

The Ammonia Level

First, there’s the ammonia level. Ammonia levels must be properly managed at all times to ensure the water is habitable for the fish you plan to keep. Many people like to maintain a zero level since it signifies the best possible conditions for fish. 

Realistically, a complete zero-level is impossible, and it’s not even advisable to try. While the ammonia is bad for the fish, it’s needed by the bacteria to create nitrates. 

As a result, strive to keep the ammonia present in the water at a low, manageable level. According to the Ornamental Aquatic Trade Association, the maximum safe ammonia level in water is 0.02mg/l for freshwater fish.

Anything above this amount causes fish to undergo significantly higher stress levels. They can even sustain permanent damage to their gills. 

The Nitrite & Nitrate Levels

Following the ammonia levels, the nitrite and, even more importantly, nitrate levels are the next important thing to measure. Generally, nitrites can cause damage to fish and, as a result, shouldn’t exceed safe levels. 

On the other hand, nitrates aren’t toxic to fish. Still, it’s necessary to measure their level periodically to ensure the plants are getting enough of them.

Ammonia, nitrates, and nitrites can be measured from water samples taken from your pond. Test kits are usually inexpensive and can test the water for you.

3. Choose the Best Plants for Your System

Once you have acceptable levels of everything needed in the pond, you can finally start to truly focus on plant life. While the method of planting is important, it’s pertinent to first decide the type of plants you want in your aquaponic system. 

There are hundreds of potential plants you could choose for your aquaponic system, but the truth is, not all plants are created equal.

What you choose depends largely on your needs and whether you can provide suitable conditions for optimal growth. While it would be nice to have a wide range of the highest quality crops, it’s all moot if you can’t care for them properly.


Tomatoes are among some of the best and most popular choices of crops for beginners and veterans alike. Not only are they an attractive and colorful addition, they’re also fast-growing and less fussy than a lot of other options, making them a good starting point on your aquaponic journey.

However, while tomatoes are low maintenance, they still require a bit of attention to yield the best results. For instance, you must consistently maintain your water at the optimum temperature.

The ideal range for tomatoes lies between 75-85 °F (23-29 °C). They might have stunted growth at higher temperatures, not growing past a certain point or refusing to turn red.

Tomatoes also require optimal pH to ensure that they grow properly. The best pH for them usually lies in the 5.5-6.6 range.

Naturally, this immediately excludes a slew of other fish and plants from the system if you want the tomatoes to grow optimally. For example, trout is unlikely to do well with tomatoes because it requires pH on the lower end of the scale.


Lettuce is yet another popular choice for people looking to grow low-maintenance crops. Like tomatoes, they require minimal maintenance and are a very good choice when just starting on your aquaponics journey.

If you plan to grow lettuce, the most important thing to get right is sunlight. Lettuce loves the sun, requiring at least five hours of sunlight every day. Notably, lettuce goes very well with the previously mentioned tomatoes, and these two are easily grown together.

Lettuce has a pH requirement between 5.8-6.2, which lies well within the safe range for tomatoes. Similarly, it can also grow at 73.4 °F (23 °C) like tomatoes, making the two a pretty decent match if you want to grow them for your system.


Peppers of all types are tricky to grow traditionally due to their requirements. They require quite a lot of sunshine and are very particular about the type of water they accept. Surprisingly enough, they thrive in aquaponic systems, provided you have the patience and attention to detail required to grow them.

Pepper is a blanket term that covers hundreds of different types of plants. If you want to be particular and grow the best for an aquaponic system, then the choice to go with would be capsicum. However, most peppers will grow well in an aquaponic system if they receive adequate care.

For the water pH, peppers thrive between 5.5-6.5, a wide enough range to ensure that they can mix in with quite a few other plants. They are pretty hardy and can handle temperatures between 60-80 °F (15.6-26 °C), with the hotter peppers able to withstand even hotter temperatures. 

Peppers will also grow to quite a height, with some reaching up to 3 feet (0.91 meter). They will also likely need the same amount of space horizontally, so you will need to watch the spacing between them to ensure that each plant has enough room to grow.


Cucumbers are yet another good choice for any aquaponic system. They’re hardy, relatively easy to grow, and survive over a wide range of temperature and pH.

Cucumbers are unique from the other crops on this list in that they don’t have very extensive root systems, which can quickly get out of hand if not taken care of. Thus, if you plan to grow cucumbers, it’s important to prevent the roots and vines from getting overgrown, as they can clog your water system. 

Cucumbers like slightly acidic water. Usually, anything between 6.0-7.0 guarantees a positive outlook for the future of your crop. 


Aquaponics and watercress go hand-in-hand. Watercress is a green leafy vegetable that loves water, making it near perfect for aquaponics. It’s also very widely used and tends to be costly in some areas, so growing it yourself is an excellent choice.

If you plan to grow watercress, be prepared to provide a bit of maintenance. These plants grow very quickly, so you must stay alert and be ready to harvest before their growth spirals out of control or crops are lost.

Watercress grows well in slightly acidic to slightly alkaline media with a preferred range of 6.5-7.5. Also, similar to most other plants on this list, they love sunlight and need quite a bit of it each day. If you live in a place where they can’t get enough sun, it may be necessary to invest in some grow lights to meet their needs. 

4. Plant Your Seeds Using an Appropriate Technique

It’s all well and good to know the best crops to plant. However, it’s equally important, if not more so, to know the best techniques to plant the seeds after you’ve decided on the ones you’d like to plant. 

Direct Sowing

Direct sowing is the easiest and most common method of growing aquaponic plants. For some people, it’s all they need. It’s also a good starting point if you’re a beginner to aquaponic as it vastly reduces the potential difficulty involved when planting.

Direct sowing involves planting seeds directly in the grow media and waiting for them to germinate. In this case, growing media is usually some form of material like gravel or pebbles. This media protects the seeds and provides the support the plant needs once it germinates.

For things like beans, it’s best to plant them piecewise, ensuring each seed gets to the moist layer beneath the growth media. However, for finer seeds like carrots, simply broadcast them over the media and pat them down after.

The main disadvantage to this method is that quite a few seeds might not germinate properly–if at all. To counter this, be sure to plant more seeds than necessary, knowing that not all of them will come to term.


Starter plugs are a great choice for seeds that are a little finicky, like peppers. Most of the time, it’s not recommended to plant them with direct sowing unless you’re accepting of an extremely low success rate.

To circumvent this, use a plug to boost the crop’s chances of coming to term. These plugs usually come in the form of materials like peat and rockwool. The main function of the plug is to provide a separate environment outside of the grow media where your crop can germinate as you tend to it. 

To use a plug, simply get the seed you want to plant and place it just beneath the fiber’s surface. After doing this, place it separate from the rest of the plant in your grow media so it gets unique attention from you. Keep in mind, using this method requires a lot of time separately to ensure the seed germinates. 

No planting method gives a guaranteed success rate. But by taking the time to plant your crop in a separate plug before moving it to the growing media can be the difference between life and death for the crop.


If you’d like to practically guarantee success for a particular crop, then one of the best options is to transplant seedlings into your aquaponic system. Transplanting involves moving germinated seedlings from an external source into your aquaponic system. Usually, this process is stress-free and can be done in a few simple steps.

Here’s how to transplant in an aquaponic system:

Get Seedlings

You have a few options for obtaining seedlings. You can either get them from an agriculture shop to get them cheaply or grow them yourself in a separate medium.

Make Space for It

Hollow out a space for the seedling you want to transplant. This step requires making proper space for the seedling to ensure the best chance of survival. Essentially, you must provide enough space so the seedling won’t struggle for nutrients.

Rinse It in a Water-Fertilizer Mix

Next, you should rinse off the seedling. This step can be optional depending on preference, but it’s a great way to boost your seedling’s growth. Rinsing your plant in a water-fertilizer mixture will help both the roots and the rest of the plant grow significantly better than they would otherwise.

Carefully Plant It

Place the seedling in the space you’ve made for it, taking care not to damage its roots during the transplanting process. Once you’re happy with its position, cover up the roots with the media around the crop.


Cuttings and clonings are the final way to grow plants in an aquaponic system. Using a cutting is essentially taking a part of another grown plant and using it as a seed. The best part to take out of the plant varies depending on the type of plant involved. 

5. Maintain Proper Conditions to Yield a Successful Yield

Taking care of your seeds doesn’t end with planting them. To have the best yield when it’s time to harvest, you’ll need to give them adequate care from when you plant them to when you’re ready to harvest.

The following list is by no means exhaustive, but it highlights some of the popular things you should always keep an eye on:

  • pH level
  • Nutrient level
  • Trimming overgrown plants
  • Maintaining proper water flow
  • Adequate sunlight or artificial lighting

Key Takeaways

Successfully starting your aquaponic seeds and good aquaponic system requires far more than just good crops. To give your crops the best chance of surviving, you must lay the proper groundwork for the entire aquaponic system.

Also, there are many crops and planting methods depending on preference and your aquaponic needs. Direct sowing is the most straightforward, but each has its merits. Regardless of what method you choose, ensure each step is done properly to yield the best results.

Alexander Picot

Alexander Picot is the founder of and its lead content writer. He created the website in 2022 as a resource for horticulture lovers and beginners alike, compiling all the gardening tips he discovered over the years. Alex has a passion for caring for plants, turning backyards into feel-good places, and sharing his knowledge with the rest of the world.

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