A Beginners Guide to Greenhouse Aquaponics

graphic depicting a raft filled with small green sprouts and roots dangling in water with 3 goldfish

Aquaponics is a growing method that combines aquaculture and hydroponics. Aquaculture is the process of raising fish and hydroponics is a soilless growing method. In short, aquaponics uses the wastewater created by fish in an aquaculture system as fertilizer for hydroponically grown produce in a recirculating system. This type of system allows you to reduce the need for added fertilizers, use water more efficiently, and sustainably grow produce. Greenhouse aquaponics adds even more benefits due to the extended growing season, protection from wildlife and certain pests, and the controlled environment. The controlled environment of a Growing Dome creates ideal conditions for both fish and plants making it ideal for greenhouse aquaponics.

Components of a Greenhouse Aquaponics System

Fish Tank

The size of tank needed in a greenhouse aquaponics system depends on a few different factors. Fish species and density, system type, size of grow beds, plant requirements, and physical space available. Luckily the Growing Dome includes an above ground pond that can be adapted to use in an aquaponics system, or you can choose to forgo the pond and install a tank specifically designed for aquaponic use. We have seen examples of both! Milk and Honey Farm utilizes the standard above ground pond in their system, while Santa Fe Community College has opted for an aquaponics tank.

Man pointing to an automatic fish feeder with an above ground pond and aquaponics system surrounding him
Standard above ground pond being used in a greenhouse aquaponics system

Types of Aquaponics Systems and Grow Beds

There are many different types of aquaponic systems available and the main difference is the style of grow beds. Determining the amount of space that you have to work with and your budget will help you choose the best system design for your circumstances. 

Media-Filled Beds

This is the most common type of aquaponics system, using a container filled with a medium such as leca (lightweight expanded clay aggregate), lava rock, gravel, or vermiculite. Plants are placed in the media, which supports their roots. The media also acts as a biofilter, breaking down fish waste into nutrients for the plants. Water from the fish tank is pumped into the bed and then drains back, often using a bell siphon or a timed system. This type of system is very versatile and suitable for a wide range of vegetables from leafy greens to fruiting plants.

Lettuce, mustard greens, and chard growing in a leca filled wooden media bed
Leca Media Filled Bed
small bright green pea sprouts in a red lava rock filled media bed
Lava Rock Media Filled Bed

Deep Water Culture (DWC) or Raft System

14" green floating island planter with four types of lettuce floating amongst frog bit in a Growing Dome pond

In this type of system, plants are placed on floating rafts in a channel or trough of water, with their roots suspended directly in the water. Water from the fish tank flows through the troughs, providing constant nutrients to the roots. This type of system is best for fast-growing leafy greens such as lettuce, kale, and basil. You can easily implement this system in your Growing Dome using our floating planters in the above ground pond or you can create a more high-tech table and raft system.

Nutrient Film Technique (NFT)

Not to be confused with the new fangled digital assets that are being traded, NFT systems utilize long, narrow channels or tubes. A thin film of water flows along the bottom of these channels, providing nutrients directly to the plant roots. It requires precise control to ensure roots stay moist without becoming submerged. This system is also best suited for leafy greens and herbs.

Romaine lettuce plant with roots exposed to show the NFT raft that is is growing in

Vertical Towers

2 homemade vertical aquaponic towers with 5 and 6 white pvc tubes oriented horizontally at slight angles to allow water to flow from the top pipe, through the middle pipes, and down to the bottom

In a vertical tower systems often using a trickle-down water system where water is pumped to the top and flows down through each plant level. Water and nutrients drip down from the top, ensuring each plant gets its share. This system is space-efficient and ideal for maximizing production in limited areas. It is also great for a Growing Dome due to the additional vertical space that you have compared to a traditional greenhouse. This system can be used to grow a variety of plants, but ones with smaller root systems do best.

Hybrid Systems

Lastly there are hybrid systems that combine elements of different systems, such as a media bed for solids filtration and biofiltration, with DWC or NFT for plant growth. This allows the benefits of each system to be utilized. In this case, the biofiltration of media beds and the efficient space use of NFT or DWC. This type of system is best for those looking to optimize space and resource use, or to experiment with different plant types. If you are interested in learning more about hybrid systems, you can look into flood and drain systems, constant height one pump systems (CHOP), ebb and flow systems, and dutch bucket systems.

Water Circulation and Filtration

A reliable pump is key to water circulation in any aquaponics system and having a backup on hand is highly recommended. When considering which pump would be best you will want to look at the flow rate to make sure it is adequate to circulate water through the entire system. Submersible pumps are often used due to the ease of installation and operation. However, larger systems may benefit from an external pump.

Also consider head height or the highest point of the system. The pump must be capable of pumping water to the highest point of the system. This is especially important in vertical aquaponics systems. Some pumps can also aerate the water, but you may need to add an additional aerator to your set up.

Mechanical and biological filters are used in aquaponics to keep water clean and nutrient-rich. Mechanical filters remove solid waste and uneaten food from the water to prevent clogging and maintain water clarity. Common methods include using screens, settling tanks, or filter pads. Biological filters use beneficial bacteria to convert ammonia from fish waste into nitrites and then nitrates, which plants use as nutrients. Biological filters require adequate surface area for bacterial colonization, such as bio balls, gravel, or specially designed filter media.

A blue AST fish tank with pipes running to a bead filter and other mechanical filers in a Growing Dome

Setting Up a Greenhouse Aquaponics System

Location

Choosing the best location for your aquaponics system depends on a couple of factors. Light exposure and stable temperature are imperative to a successful aquaponics system. You want to make sure that your plants are getting proper sunlight throughout the year and that they are not subject to significant temperature swings. Therefore the best placement for an aquaponics grow bed in a Growing Dome is in the central region and the best position for the tank is along the north wall. 

You will also want to make sure that the system is easy to access for maintenance and daily tasks like feeding fish and harvesting plants and that it is also close to utilities. Consider running utilities to your Growing Dome site prior to building the greenhouse. Ventilation is also key in any greenhouse and especially in one that is using aquaponics as the main growing method. Check out our greenhouse ventilation guide to determine the best options for you!

Ideal Plants and Fish

6 goldfish surfacing for food in a pond filled with green frog bit

When choosing fish for an aquaponics system you will want to think about the water temperature in which they thrive as well as dietary requirements. Not all fish are the same. Tilapia are a popular choice because they can also be harvested for consumption, but need warm water and reproduce quickly. Bass are also popular and can be consumed, but require more protein in their diet than other fish.

Our go-to fish are goldfish and koi as they are hardy fish that can tolerate a wide temperature range. However, they are ornamental and are not harvested for consumption. The number of fish you have is going to depend on the size of your greenhouse aquaponics system and the size of the fish themselves. For example, you will need far fewer koi than goldfish.

When it comes to plants, again it depends on your system and grow bed design. We mentioned which plants grow best in each system above, but in general “heavy feeders” or plants that uptake the most nitrogen will be best. These include nightshades (tomatoes, peppers, eggplants), brassicas (cabbage, broccoli, kale, cauliflower), strawberries, leafy greens (lettuce, arugula, spinach, watercress), and herbs (cilantro, parsley, basil, mint). Cucurbits (squash, melons, cucumbers) can be grown aquaponically, but require a lot more space than other crops.

Many tall tomato plants full of fruit of varying ripeness growing in a Growing Dome using a greenhouse aquaponics system

Initial Cycling Process in a Greenhouse Aquaponics System

The initial cycling process, also known as “fishless cycling”  is one of the most important if not the most important step to setting up an aquaponics system. In the most basic of terms this process regulates the system before adding any plants or fish. You will start by filling your system with water and letting it run for a couple of days. This helps to stabilize the temperature or the water as well as the pH. Optimal water temperature is between 65-85°F and pH should fall between 6.5-7.2.

Next you will check your ammonia, nitrate, and nitrite levels. You are looking for ammonia levels to fall between 3-5 ppm. If your levels are lower than the desired range you will need to add pure ammonia into the system.

Beneficial bacteria will grow naturally over time, but you may decide to add nitrifying bacteria into your system to speed up the process. These bacteria convert ammonia into nitrites and then into nitrates. You will likely see a spike in nitrites during the beginning of this cycling process which is why it is so important to complete this process before adding your fish. Nitrite levels should be less than 1 ppm because nitrite levels above 5 ppm are toxic to most fish. Nitrate levels should be between 30-60 ppm. 

The whole initial cycling process can take 4-6 weeks to complete. You will know your system is ready when ammonia and nitrite levels drop to zero or near zero and the nitrates fall into the desired range. You can then start to slowly add in your fish and plants. Be careful not to overload the system. Adding too many fish at one time can cause excess waste that the beneficial bacteria cannot process which will throw off the delicate balance of the ecosystem. Adding too many plants can uptake the nitrates before the bacteria have a chance to make more. 

Maintaining a Greenhouse Aquaponics System

Once the system is set up the maintenance should be minimal. The number one priority is making sure the fish are fed and that both the fish and plants are healthy. Having sick fish or sick plants can disrupt the entire system. 

API Freshwater master test kit resting on a flagstone covered water feature in a Growing Dome pond filled with floating plants

Check the water quality regularly. This includes nitrate, nitrite, pH, and ammonia levels. The freshwater master test kit from API is a great tool for this. You should also be checking the dissolved oxygen and temperature of the water frequently. Also check on your pumps and filters periodically to ensure they are working properly and free from obstructions.

Challenges and Solutions of Greenhouse Aquaponics

System Design and Scale

It is easy to see how one can get overwhelmed by the amount of information available and the many different types of aquaponics systems. Beginners may overcomplicate the system and scale it too quickly. Our best advice is to start small and simple. Once you have mastered the balancing of nutrients, fish, and plants, then consider scaling up.

Pests and Diseases

Pests and diseases can impact both fish and plants in an aquaponics system. When it comes to plant pests, an integrated pest management approach is recommended. You do not want to use any chemical pesticides that may harm your fish, so mechanical, biological, and cultural controls will be needed. Fish can develop diseases, so it is a good idea to have an isolation tank ready. This will allow you to remove any ill fish and nurse them back to health before reintroducing them into the system.

Seasonal Changes

Controlling temperature is key to a successful greenhouse aquaponics system. You will likely need to invest in some sort of climate control whether that be cooling systems for summer, heating systems for winter, or both. Many of our customers that have greenhouse aquaponics systems, such as The Aquaponics Project at Chesapeake Bay Environmental Center and Lacombe Composite High School, also have a climate battery or a GAHT system. These types of systems harness the stable air temperatures below ground to keep the greenhouse warm in the winter and cool in the summer.

Additional Resources and Recommended Suppliers

We will admit we are not aquaponics experts. We have dabbled in the art of greenhouse aquaponics, but at the end of the day, we are Growing Dome experts. There are a few companies that we highly recommend that have the expertise to help you with any further questions.

The Aquaponics Source has online classes, tons of resources and videos, as well as supplies to set up your system. Aquaculture Systems Technologies (AST) systems have been used in many successful Growing Dome greenhouse aquaponics systems. They have done all of the research needed to create a high-tech yet simple-to-use system. They have great videos and offer free consultations.

author avatar
Shelby Lucero Social Media Coordinator
I graduated from Fort Lewis College in 2018 with a BA in Environmental Studies. I began working for Growing Spaces in August of 2020 and have had the pleasure of working in many departments. I enjoy being a part of this amazing team that helps others achieve their dream gardens! In my spare time, I enjoy working in the 15’ Growing Dome that my husband and I share.

1 Comment

  • Most aquaponics systems keep the fish tank in the shade. The thermal storage tank in a Growing Spaces dome is exposed to direct sunlight in the winter and indirect light in the summer. This light onto the nutrient rich water (nitrates, etc) will produce an algae bloom unless the algae are controlled. I have found that a UV filter after the particle filter works very well to control the algae and other harmful bacteria. This is a common solution for koi ponds which have the same problem.

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