As with aquaculture, hydroponics is a well-established industry, decades ahead of aquaponics in terms of commercial development and fundamental research. The most effective aquapioneers out there know this and leverage the decades of experience from the soilless farmers before them when considering system design.

There is a diverse array of tried-and true hydroponic grow methods. They can be broadly categorized into three groups, deep water culture (DWC), media beds, and vertical farming.

Deep Water Culture

The most established form of hydroponic growing in aquaponics systems is deep water culture (DWC). DWC growing consists of troughs of water and floating rafts, which house the plants in a strategic array of holes across the raft board. DWC is great for growing leafy greens in the conveyer crop style. Some aquapioneers like Ryan Chatterson of Chatterson Farms has proven DWC to be super effective for fruiting crops as well.

Our favorite crops for DWC:

  • Leafy greens and asian greens
  • Basil, parsley, sage, and other stemmy herbs
  • Expert aquaponioneers like Ryan Chatterson have proven season after season that DWC is totally capable of amazing fruit crop production including tomatoes, cucumbers, squash, and more.

DWC troughs are typically twelve inches (12”) deep and four feet wide.

They are typically built lengthwise in increments of two feet because the typical grow raft is 2’x4’. 

DWC troughs can be built DIY style from wood and pond liner or with modular products like the Raftmaster from Bigelow Brook Farm.

DWC troughs can be purchased as prefabricated parts from many hydroponic suppliers. Please note, the recommended depth of aquaponic DWC beds is roughly 12” and typical hydroponic trough products are 6” or 18”.

DWC troughs include aeration as an extension of the air pump in the aquaculture section. We usually run an airstone for every 4 linear feet of grow trough length.

Designer’s Note: DWC troughs make very effective sump tanks! Just place a pump in the last DWC in the flow cycle and voila! It is the sump tank. 

DIY rafts can be cut from 4’x8’ boards of blue Dow Insulation Board. Make sure it’s the blue board! Pink and other colors can be toxic in aquaponics systems, whereas the blueboard is non-toxic and has been tested for years by dozens of aquapioneers. Professionally manufactured raft boards are available from a number of suppliers online.

Each raft holds a specific number of plants. High efficiency designs have a certain proportion of rafts as high-density (~110 slots) for young plants entering the system. As these plants grow, their roots need proper spacing to help optimize nutrient uptake. They are moved to rafts with 32 holes, which allows for generous spacing to accommodate full growth by a wide variety of plants. At that spacing, you can increase your grow capacity by over 70% by using a seedling raft for young plants rather than a full size raft..

Media Beds

The defining features of media beds are the large trays of growing media that periodically flood with nutrient water then drain to draw air into the growing media. The periodic flooding is why media beds are also known as ebb-and-flow or flood-and-drain systems.

Media beds in aquaponics are typically 12” tall. This size creates multiple distinct stratifications in the media bed: 

  • The top 1-2 inches is above the waterline and provides a dry root zone.
  • The bottom inch is nearly always wet and may sometimes contain anaerobic pockets which can help release minerals into the system, if handled properly.
  • The root zone is the space between the top and bottom layers. It floods and drains, which alternatively provides hydration and nutrients to plants, followed by aeration, so as not to drown the roots.

Our favorite crops for media beds:
We like to use media beds for crops that require large root systems, have excessive growth that may oddly weigh down a DWC raft or vertical tower, or plants that don’t like wet feet. Radishes and carrots are two!

How to create a reliable flood and drain cycle: Timers vs Siphons
Timers are very common in standard hydroponics and for good reason, they are reliable, time tested, and can easily dictate pump times. A typical hydroponic farmer will run flood cycles for 15 minutes at a time and drain cycles for 45 minutes.
Timers are also used in aquaponics plant growing, but media beds are not a significant portion of total commercial aquaponic grow space, so they are less prevalent. Additionally, the typical 15:45 flood:drain cycle is not as viable in aquaponics compared to chemical hydroponics. When using a timer in aquaponics, try to flood and drain the beds more often, cycling at least 4-10 times per hour.

Siphons are more common in DIY aquaponics media beds. Siphons are a term for a category of tools that use the siphon effect to suck the water out of a flooded media bed automatically using pressure instead of electricity.
The most common type of siphon is known as the bell siphon. We prefer Affnan’s Bell Siphon, which uses vortex dynamics to create a fail-safe siphon that bypasses the tendency for bell siphons to fail over time.
Siphon media beds are constantly fed water without a timer. The media bed fills up and eventually enters the standpipe in the bell siphon. As the flow increases, the bell siphon engages and sucks all of the water out of the media bed. We like our media beds to flush four times an hour minimum.

Media beds were introduced to us by Murray Hallam of Practical Aquaponics in Australia. Murray played a large role in popularizing IBC aquaponics. IBCs, or intermediate bulk containers, are very common containers used for shipping liquids. They can be found locally in many areas across the US and abroad. We buy ours on craigslist! IBCs are 3’x4’x4’ plastic cubes mounted on a pallet and surrounded by an aluminum support cage. They can be used as great DIY fish tanks, but are most commonly used as media beds. The bottom and top 12” of the IBC can be chopped off and used as a perfect media bed container. My first backyard aquaponics system was with IBCs and siphons; it still holds a warm place in my heart.

Vertical Farming

Vertical farming refers to the many methods that grow plants in multiple layers on top of one another in the same square foot. There are two distinct categories of vertical farming we would like to highlight, we call them horizontal-vertical and vertical-vertical. The distinction comes from the way water flows through each vertical system. Horizontal-vertical systems refer to systems consisting of vertical stacks of horizontal grow areas. Vertical-vertical systems refer to tower gardens where water flows from the top of the tower straight down towards the catchment basin at the base of the tower. 

Stacked grow trays, similar to shallow media beds, are a common form of hydroponic vertical farming. Companies like Aerofarms have received large investments to construct massive farms dedicated to hydroponic farming in this style. Typically these stacked trays are 4-8” and used to grow small, leafy green crops like baby lettuce and microgreens. Stacked trays can also be shallow DWC beds, rather than shallow media beds. Seeding areas for commercial farms are usually grown this way by replacing the shallow plant beds with seeding trays.
Most popular crops in stacked trays:

  • Baby greens, i.e. normal greens like kale, harvested early in life cycle
  • Leafy greens
  • Bushy herbs

Nutrient Film Technique (NFT) refers to horizontal tubing with plant holes drilled in according to the desired plant’s space requirements. A low trickle of nutrient laden water runs horizontally through the NFT channel and the roots dangle into it from the plants in the plant holes. NFT channels can be stacked vertically to easily take advantage of vertical space in tight areas. NFT also lends itself to DIY users because they can easily be constructed from common PVC plumbing.

Most popular crops in Nutrient Film Technique:

  • Bushy and vining fruiting crops do great because of the extra aeration from being suspended from the NFT channel

Vertical Towers are an emerging method of vertical farming, popularized by companies like Bright Agrotech (facebook) and Freight Farms (facebook). These companies use the ZipGrow tower, developed by Dr. Nate Storey (founder of Bright Agrotech). The ZipGrow is a unidirectional tower, meaning the plants grow out of only one side. The remaining three sides are reflective white food-grade plastic, which helps reflects light within an array of towers. Dr. Storey has spent his career proving out the commercial viability of unidirectional towers like his ZipGrow. We love using the ZipGrow tower in a large number of our projects because they are easy to use and highly space efficient.

Multidirectional towers or 360° towers offer grow space on every face of the tower. These towers require novel lighting solutions because sunlight will always neglect at least one side of the tower. Likewise, these towers require artificial light from multiple directions in CEA facilities which increases complexity of the system. It is unclear whether the supposed increase in plants per tower actually results in an increase in production, especially when the above inefficiencies are taken into account.

DIY vertical towers are popular on Youtube because they are easy to make from common materials like PVC piping and allow people to grow a decent harvest in even the most cramped grow areas. We experimented early on with DIY vertical towers and eventually moved on to the ZipGrow towers because it was easier to work with a professionally crafted product.

Our favorite crops in towers:

  • Leafy greens, asian greens, kale, stemmy herbs, and bushy herbs


All of the diverse forms of hydroponic farming share one commonality, they require nutrient-laden water supplied through irrigation plumbing. We know the nutrient water is being supplied by the aquaculture and filtration systems. It enters the hydroponic system either a) via gravity from the clarifier, or b) from the pump in the sump tank.

Irrigation comes in many forms and is most commonly made from common PVC of various sizes or ½” or ¾” water pump tubing and standard hydroponic fittings.

Clogging is a real concern in aquaponics systems. Tubes clog from buildup of solid fish waste as well as slime molds, which are naturally occurring globs of symbiotic microbes. The smaller the tube, the more likely you are to clog. ½” tubing will have to be massaged to preventatively break up clogs every few weeks. We recommend a minimum of ¾” -1” tubing to reduce this buildup. 

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