The How-To of Organic Hydroponics

By Lynette Morgan
Published: December 28, 2020 | Last updated: December 7, 2021 10:19:06
Key Takeaways

Running a successful organic hydroponic system involves some trial and error. Learn how to get started.

Source: Pokko3 /

There is a long-standing debate as to whether soilless hydroponic systems can ever be completely organic. For the most part, this debate is the result of disputed ideas about what organics actually means. Even in the commercial horticultural world, things are not clear-cut when it comes to what is and what isn’t considered organic.


In many parts of the world, certified-organic systems must have soil as the cornerstone of their production. In the United States, certain types of hydroponic systems can become organically certified without the use of soil.

While the reasoning behind whether or not hydroponics is organic is still under debate, hobby growers need not bother with the large-scale logic. Instead, they should decide what organics means to them and follow techniques to fulfill their own ideologies.


For some growers, producing organic and natural crops from an indoor garden simply means avoiding the use of toxic chemicals such as synthetic pesticides, fungicides and sterilization agents. These types of growers choose to focus more on natural approaches while fully embracing hydroponic methods.

For others, growing organically means incorporating the use of organic nutrients combined with beneficial microbial populations similar to the methods used by soil-based organic producers. Unfortunately, it’s not just a simple case of switching from traditional, fertilizer-salt-based nutrients to organic ones since many early hydroponic systems were never designed to be used with organic compounds and many growers have run into major issues when trying this.

Read More: Beneficial Microbe Populations in the Indoor Garden


Traditional hydroponic nutrients are made from fertilizers such as calcium nitrate, potassium nitrate, monopotassium phosphate, iron chelate and many others that, when dissolved into water, dissociate into ions ready for immediate uptake by plants. This is what allows for such rapid and balanced plant growth.

The plants never have to starve or wait for nutrient ions to become available. However, calcium nitrate and many others used in traditional hydroponic systems are not considered organic, but synthetic or man-made, and are not part of an organic system.


Replacing highly effective and carefully calculated fertilizer salts with organic nutrient sources is not easy. Manufacturers of hydroponic fertilizer products go to great lengths to get the ideal parts per million of each nutrient ion in their products so plants grow as fast and balanced as possible.

With organic nutrient sources, it’s impossible to be so precise, so mineral deficiencies within organic hydroponic systemsare often an issue. Also, organic nutrients contain a great deal of carbon, which non-organic nutrient products do not provide. This carbon is an ideal source of food for microbes in the nutrient solution and root zone, feeding both beneficial and pathogenic fungi and bacteria.

If unwanted microbes begin feeding on the carbon from organic nutrient sources, things can get a little toxic, creating slimy nutrient solutions, anaerobic root conditions, diseases and even plant die back. To avoid these problems, organic growers just starting out should begin slowly and with systems known to have a better success rate.

Suitable Hydroponic Systems and Growing Mediums

Among the most successful systems for organic hydroponics are aquaponic systems. If the system is run with the correct fish-to-plant ratio and a good rate of mineralization carried out by specific bacteria, aquaponics is one of the easiest approaches to organics.

Novice growers should start with low-nutrient-demanding crops, such as lettuce, salad greens and fresh herbs, and gradually build up to fruiting plants as the system matures and higher rates of mineralization occur. Even though aquaponic systems provide good levels of nutrient ions from fish waste, high-nutrient-demanding crops may still need a little supplementation, especially extra trace elements from time to time.

Read More: How to Start an Aquaponics System

Aside from aquaponics, many successful, organically certified commercial hydroponic systems incorporate the use of a natural growing substrate to support the plants and provide a high surface area for the large population of microbes needed to process (mineralize) the organic fertilizer sources.

Many of these mediums use coconut fiber as a base because it is a natural material amended with a range of other substrates such as high-quality composts, vermicast (worm castings), perlite, bark, peat, vermiculite and even rice hulls. There are also organic growing mixes on the market specifically designed for hydroponic systems.

It is important for the growing medium to be free-draining and highly aerated. It should ideally contain some already-mineralized nutrients (compost and vermicast), and be a source of naturally occurring beneficial microbes, or have them inoculated in before planting occurs. A good medium for organic production has proven to be a mix of coconut fiber, coarse perlite and high-quality, fully-processed vermicast (20%) to provide some immediately available nutrients and diverse microbes that will process the organic nutrient solution when it is applied.

New organic substrates incorporated into a hydroponic system should be conditioned before use—fully moistened, inoculated with microbes, fed a small amount of organic nutrients and left to sit in a warm growing area for at least 1-2 weeks before planting out. This gives microbial communities time to establish and build up numbers before starting to break down organic compounds into plant-usable nutrient ions ready for the first plants to go in.

Once plants are in place, the irrigation system needs to be run a little differently than traditional, non-organic hydroponic systems. Drip irrigation at the root zone is advised. The root zone should never be over-saturated; only a small volume of leachate from the base of the growing containers is required.

A plant’s root zone in organic systems is finely balanced between the requirements of the microbes and the root system itself. Both require high levels of oxygenation, and overwatering excludes much of the aeration in the pores of the growing medium.

Organic systems have a higher requirement for oxygenation in the root zone due to the heavy populations of microbes required. Many failures in organic systems are directly related to overwatering and poor aeration.

EC and pH Levels

Electrical conductivity (EC) and pH control is also different in organic hydroponic systems. Many organic nutrients don’t conduct electricity, so EC readings may not be a true indication of the concentration of an organic solution. A garden’s pH levels also tend to run higher in a healthy, organic system than many growers are used to maintaining in standard hydroponics.

Since pH-lowering acids commonly used in hydroponics such as nitric and phosphoric acids are not organic, pH is best left to stabilize on its own. Some organic nutrient products naturally have a high pH, so growers should try to select those that have a more suitable pH range for use in soilless systems.

Organic Nutrients

There are a few different approaches to obtaining and using organic nutrient sources in a hydroponic system. It can be difficult to get a balanced and suitably high ratio of all the essential minerals from organic sources alone, so experimentation with different products is helpful. There is a range of liquid organic nutrient concentrates on the market, as well as some fertilizer salts that are considered organic and naturally occurring to help boost growth where required.

Generally, sulphate trace elements, such as iron sulphate, copper sulphate, zinc sulphate, manganese sulphate and magnesium sulphate (Epsom salt), are allowed under organic production, so these can be used to help round out any deficiencies that may occur with organic nutrients.

An organic iron chelate can be made by mixing iron sulphate with citric acid powder to replace the synthetic iron chelate (EDTA or DTPA) commonly used in traditional hydroponics to ensure ongoing iron availability. Growers often need to blend two or more organic liquid fertilizers to provide sufficient and balanced nutrient levels for most hydroponic crops.

An organic base product (often a concentrated fish emulsion base or similar) blended with an organic liquid calcium is a good place to start. An organic nitrogen product may be required later on. Growers should aim to use products that have been designed for soilless systems wherever possible.

The main difficulty with running organic systems is obtaining sufficient amounts of nitrogen and calcium, which are required in large amounts by plants. Organic systems rely on microbes in the root zone to convert organic compounds into plant-available nitrogen sources and sometimes this process does not occur fast enough for uptake.

Calcium is difficult to obtain rapidly from organic nutrients as it relies on the breaking down of calcium-containing materials such as limestone. Growers who have hard water sources containing naturally occurring calcium have a major advantage in this case because this form of calcium is readily available for plant uptake.

It is possible to make an organic nutrient solution completely from raw materials rather than relying on commercially bottled products. While liquid bio-digesters that turn raw organic materials into usable plant nutrients have been used by some growers, the more reliable method for smaller systems is vermiculture (worm farming).

Vermiculture is a highly efficient way of processing high-mineral raw materials, such as manures, limestone, blood and bone, fish meal, seaweed meal, guano and others, into usable, mineralized hydroponic nutrient solutions that also provide the benefits of a diverse population of beneficial microbes.

The successful use of vermiculture to process organic fertilizers relies on two things. First, the vermicast must be processed to completion and then extracted into water for use in a hydroponic system. The extract or liquid draining from the vermicast system should not be used as a nutrient solution until the vermicast itself has been fully processed.

Many worm juices on the market are highly diluted and often not balanced enough to use as a stand-alone nutrient solution. Second, the quality of the raw materials going into the vermicast system will determine how balanced the final nutrient will be. High-mineral sources, such as fish, blood and bone meal are often dried and ground into products, while food scraps, weeds and vegetation contain only low levels of minerals and will not make a nutrient solution concentrated enough for most hydroponic systems.

One of the main problems with organic nutrients is concentration. Most organic liquid products are not as concentrated as standard, salt-based fertilizer formulations, so plants may become weak, stretched and more prone to disease.

Growers need to be aware of what underfed plants look like and boost nutrient concentrations as soon as these conditions are detected. Nutrient additives and boosters, such as humic acid and fulvic acid, are a good addition to organic systems as they help facilitate nutrient uptake and are generally considered organic.

Pest and Disease Control

Once growers have established a healthy root zone and are feeding plants a suitable organic blend of nutrients, the next step in organic production tends to be pest and disease control. Synthetic or chemical pesticides and fungicides are not considered organic, which eliminates some of the highly effective controls many hydroponic growers depend on.

With organic production, prevention of pest and disease problems becomes even more essential. The use of screening vents, double-door entries, close inspection of planting material entering the growing area, sticky indicator traps and careful monitoring of plant health are essential in preventing or catching infestations early on.

Among the organically allowable pest control products, many indoor gardeners are already familiar with neem oil and extracts, which are derived from the Indian neem tree. Many neem spray products are considered organic and help control a wide range of insect pests.

Beneficial and predator insects as part of an integrated pest management program are also widely used by organic growers, and there are a range of microbial spray products on the market such as bacillus thuringiensis (BT) for caterpillars.

Disease control can be little more complicated. Fortunately, biological controls like Beauveria spp. and other non-synthetic fungicides based on microbial species are available. Local hydro shops will have more information on all of these options.

Running a successful organic hydroponic system involves some trial and error. What works for one grower may not work for another. There is a lot more to the biological side of organic plant nutrition than we understand, much of it to do with microbial balance and populations in the root zone and nutrient solution. Overall, being successful in organic production is an exciting achievement and is one more growers are experimenting with.

Read Next: Are Organic Pesticides Always Safer?


Share This Article

  • Facebook
  • LinkedIn
  • Twitter

Written by Lynette Morgan | Author, Partner at SUNTEC International Hydroponic Consultants

Profile Picture of Lynette Morgan

Dr. Lynette Morgan holds a B. Hort. Tech. degree and a PhD in hydroponic greenhouse production from Massey University, New Zealand. A partner with SUNTEC International Hydroponic Consultants, Lynette is involved in remote and on-site consultancy services for new and existing commercial greenhouse growers worldwide as well as research trials and product development for manufacturers of hydroponic products. Lynette has authored five hydroponic technical books and is working on her sixth.

Related Articles

Go back to top
Maximum Yield Logo

You must be 19 years of age or older to enter this site.

Please confirm your date of birth:

This feature requires cookies to be enabled