Troubleshooting in the Hydroponic Garden

By Lynette Morgan
Published: February 1, 2016 | Last updated: April 26, 2021 11:44:51
Key Takeaways

From time to time, we all strike problems with our hydroponic systems and plants. If we are lucky, it’s an easily resolved issue that doesn’t cause too much stress. However, some things can baffle even the most experienced grower and that’s when a step-by-step approach to troubleshooting is required.

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Most common problems experienced in hydroponic gardens are caused by one of four main things: nutrition, the plant’s growing environment, pests and pathogens and—less frequently encountered—genetic problems.


Even though complete, balanced and well-formulated nutrient solutions are used in hydroponics, nutrition can still be a main area of troubleshooting and one that confuses many inexperienced growers.

Hydroponic Nutrient Troubleshooting Tips

Hydroponic systems are reliant on the composition and formulation of the nutrient solution to supply all the essential elements required for optimal plant growth and yields. However, nutrient solutions are complex and their composition changes as mineral ions are extracted when they flow through the root system.


Deficiencies in hydroponic production are more common than toxicities, as plant uptake of many elements has the potential to strip out nutrients at a rapid rate, particularly from recirculating solutions.

The most common deficiency problems in hydroponic crops are potassium in fruiting plants like tomatoes; iron under certain environmental conditions; nitrogen in some readily growing, highly vegetative crops; and calcium in many species, such as lettuce, tomatoes and peppers.

To complicate hydroponic plant nutrition further, deficiencies (as they occur on different crops) might or might not be the result of an actual deficiency in the nutrient solution.


Potassium can certainly be stripped from a nutrient solution rapidly as fruit develops and expands, and because luxury uptake occurs in many crops. However, iron, calcium and magnesium deficiencies on leaves and fruit occur even when there is more than a sufficient amount of these elements in a solution.

These induced deficiencies often fool growers into thinking there is a problem with the formulation of their nutrient when the cause is often more complex.



Iron deficiency is common under cool growing conditions, where the root system might have become saturated or damaged, or where the pH is running high.


Magnesium deficiency on crops like tomatoes can be induced by high levels of potassium uptake.


Calcium deficiency, which shows as tip burn on lettuce and blossom end rot on tomatoes and peppers, is a calcium transport problem within the plant rather than a lack of calcium in the solution. It is induced by environmental conditions like high humidity, which restricts transpiration and calcium distribution.

Salt Buildup and EC Problems in Hydroponics

Salt buildup appears as white or off-white crystalline crusts or residues on the surface of growing media and sometimes on the base of plant stems, where it can cause salt burn damage.

Certain types of media are more prone to this nutrient problem than others—for example, those with porous structures and high rates of water loss are more prone to salt crusting than others.

Expanded clay granules and similar media often develop a whitish coating on the surface after a few months use, and this can be common in ebb-and-flow systems.

Media beds covered with plastic film—as in the case of rockwool slabs—rarely develop these salt deposits on the surface, as the film prevents excessive moisture loss from the media.

Salt buildup occurs when a media, which has been thoroughly wetted with nutrient solution containing dissolved salts, loses moisture to evaporation faster than the minerals are taken up by the plant’s root system.

In this case, the moisture is lost to the atmosphere and the minerals stay behind, thus increasing the EC in the media and around the roots.

This salt buildup in the root zone can cause damage both through direct contact with the salt crystals around the delicate plant stem, particularly in seedlings, and by increasing the osmotic pressure around the plant roots.

Luckily, salt buildup is easily dealt with once growers recognize the symptoms: white crusting is the first sign, as is plant growth becoming stunted, dark, hard and unusually slow.

As salt accumulation becomes more severe, the stem area at the base of the plant and roots can be burnt and die back, resulting in wilting during the warmer times of day and, later, disease attack in these areas.

Regular monitoring of the EC of the nutrient solution draining from the media helps prevent and diagnose salt accumulation problems. Ideally the EC of the feed solution should not increase as it flows through the root system.

If the EC is increasing as its flows through the root system and out the base of the growing container, then salt buildup is likely to occur. However, even plants fed a low EC solution can develop salt accumulation where the atmosphere is dry and high rates of water loss from a porous media occur.

In this case, the media will benefit from some leaching from time to time and a thorough clean between crops (or even replacement in severe cases).

Some growers prefer to leach excess salts from growing media using plain water; however, this can have negative effects when an actively growing crop is present, as the sudden drop in osmotic pressure in the root zone triggers a large influx of moisture into the root cells, which can result in fruit splitting and soft, weak vegetative growth.

Flushing growing media with either a specifically designed flushing solution or a nutrient one-third its regular strength is recommended to remove excess salts from the root zone.

Carrying this process out every few weeks might be required in certain hydroponic systems, such as shallow flood-and-drain or tray systems in warm climates with high evapotranspiration rates, and often between crops if media is to be reused

Mow Much Algae Should I Expect to See in My Hydroponics System?

Most hydroponic growers come across algae sooner or later. It can appear as a green, brown, reddish or black, slimy growth that clings to channels, gullies and pumps or spreads over the surface of damp media.

Long strings of algae are common in nutrient tanks and return channels, and the speed at which this form of plant life can grow and multiply is often impressive.

Algae usually have earthy or moldy smells, and large volumes of decomposing algae in the nutrient can be responsible for unpleasant odors.

Algae is a nuisance to any grower as it not only looks unsightly, but has the ability to block drippers, emitter, pumps, return channels and filters. Heavy growth can even seal off the surface of growing substrates, robbing the roots of oxygen.

The problem with algae—apart from the appearance and smell problems it can create—is not so much that it competes with plant roots for nutrients, but that it sucks up dissolved oxygen from the system it blooms, dies and decomposes.

This increases the biological oxygen demand (BOD) on the system and causes root suffocation from a lack of oxygen.

Decomposing algae might also release toxins as it breaks down and provides a food source for plant pathogenic fungi, which might then multiply to high levels in the system.

Algae directly attached to plant root systems can suffocate the roots, making the plants prone to attack by opportunist pathogens like pythium.

Control of algae, once established in a hydroponic system, can be difficult. Still, most growers tolerate small amounts of algae in their systems, provided it does not become excessive.

A regular scrub between crops will often remove stubborn algae and is often the only control used by commercial growers.

Some growers do add algaecide products into the nutrient to kill off algae and there are a number of these products on the market. However, since any product that kills algae (a form of plant life) can also damage young or sensitive root systems, care must be taken with the dose.

Also, algae will regrow very quickly after applications of most algaecide products, thus requiring regular applications to maintain good control.

Suffering Roots in a Hydroponic System

The major causes of root death in hydroponics are suffocation, starvation, pathogens, chemical damage, temperature and EC/pH problems.

In hydroponics, suffocation is probably the leading cause of root death and reduced growth rates. Often, any pathogens present won’t attack a healthy root system until it is damaged or weakened by adverse conditions (such as stagnation or suffocation in the root zone).

A lack of oxygen can be caused by flooding or ponding of the nutrient solution, decomposing organic matter in the solution, slow flow rates and too many plants robbing oxygen from the root zone, which is accelerated as conditions become warmer.

A lack of oxygen reduces the permeability of roots to water, and toxins will accumulate as the root cells die. Some plants, such as tomatoes, will attempt to adapt to the lack of oxygen by producing adventitious roots on the lower stem and swelling at the stem base.

Are Your Roots Starving for Nutrients?

A lack of nutrients will affect the root system, just as it does the top of the plant; however, the symptoms are more difficult to observe.

A phosphate deficiency will cause the roots to become brown with a reduced number of lateral branches.

A lack of calcium will induce a thin, poorly developed brown root system. Manganese deficiency will cause a small root system that’s much shorter and finer than usual, with some browning of the root tips.

Copper deficiency results in severe underdevelopment of the root zone. Boron deficiency causes the root tips to become jelly-like in appearance.

EC and pH of the Root Zone

An electrical conductivity (EC) level that is too high for the crop being grown will result in severe stunting of the root system.

If the EC reaches extreme levels, water will be lost from the root cells back into the nutrient solution to the point where root death will occur. This is more common in crops that prefer a lower EC level, such as lettuce.

Likewise, pH levels that are too high or low can induce root damage and nutrient uptake problems. (Still, the pH range that plants can tolerate without any negative effects is fairly large.)

It has been found that the appearance of the root system differs in hydroponic plants that have been grown at different pH levels.

Plants grown at a pH of 7.5 and above have a shorter, coarser root system than those grown at a pH of 5.5.

Higher pH levels reduce the availability of certain elements in solution, mostly iron and manganese, and could induce deficiency symptoms.

Root Diseases

Root diseases are a major concern for hydroponic growers. This is particularly true of growers who use NFT and other recirculating systems that could quickly transport pathogens to a large number of plants.

Some pathogens that can attack roots in hydroponic systems have symptoms that make them easy to identify (with some practice). However, others might not have any symptoms at all.

One aspect these pathogens all have in common is their ability to reduce plant growth and yield.

The most common pathogens that effect roots in hydroponic production are pythium, phytophthora, fusarium, olpidium, plasmopara, didymella and verticillium.

Others have also been reported to cause crop losses; in fact, about 20 fungal, four viral and two bacterial pathogens exist that are commonly associated with root diseases in hydroponic vegetable crops.

Root pathogens can infect hydroponic crops from a number of sources, including air, water, media, insects, infected plant material, seeds and dust. Airborne root pathogens are rare, but have been known to occur.

A more common source of infection is soil, which hosts a huge number of inoculum. Soil can enter a hydroponics system on shoes, as dust in the air, in media, on equipment or in water (particularly from exposed sources, such as reservoirs, rivers and streams). Insects, such as shore flies and fungus gnats, can also carry pathogens.

Since many root problems and odd symptoms are caused by pathogens, and such attacks are often induced by stressed plants, cultivating a healthy crop is always a grower’s first line of defense.

Ensuring adequate oxygen is present in the root zone throughout the hydroponic system is essential. Sometimes environmental or cultural problems exist that stress the plants without the grower’s knowledge.

Therefore, observing the root zone on a regular basis is vitally important. In media-based systems, a grower who notices a plant showing signs of wilt or discoloration should pull it out and examine the root system.

Once any plant has been identified as potentially having a root disease, it should be removed from the cropping area and destroyed. Proper sanitation and hygiene in hydroponic systems is also important for pathogen control.

Root pathogens can carry over from one crop to the next, so many media or substrate that contained an infected plant should be discarded.

In areas where there are high populations of root disease pathogens, commercial growers need to consider some form of control, such as treating the water supply with UV light, H2O2 or ozone.

Fruiting and Flowering Problems in Hydroponic Systems

Fruiting crop problems in hydroponics can range from a simple lack of fruit development to more complex physiological disorders like blossom end rot.

Many growers have experienced fruit with skin disorders, such as uneven coloration, blotching, crazing, streaking, silvering and other unidentified spots.

Fruit splitting can be common in crops like tomatoes. Bell peppers and cucumber can become grossly misshapen. These disorders are largely physiological, environmental and cultural.

Flower and fruitlet drop

Most common hydroponic crops will flower when they have reached their appropriate point in development. One frequent problem is flower drop.

There are many potential causes of flower and fruitlet drop in hydroponic crops; some are internal and caused by plant stress, and some are environmental.

In many crops, flower drop in induced by high air temperatures. However the point at which this thermal stress occurs varies for each crop and cultivar. Low light levels that limit the growth of the whole plant can also induce drop, particularly where low light is combined with high temperatures.

Although not as common in hydroponic crops as those grown in soil, mineral deficiencies, such as low levels of nitrogen or phosphorus in the nutrient solution, can slow flower and fruit development and cause drop. Flower drop can also be caused by water stress (either a lack of irrigation or high EC levels).

With the development of high-yielding cultivars, another major cause of flower and fruitlet drop has become heavy fruit load or excessive vegetative growth.

Young, newly developed leaves compete for assimilates with the flowers and fruitlets already on the plant. If assimilates are transported to these new leaves at the expense of the flowers, drop can occur.

This is more common in situations where assimilate production is limited due to low light or other reasons.

Lowering plant density and using CO2 and suitable cultivars less prone to drop both assist growers in preventing these types of problems (which often occur in winter).

The presence of a heavy fruit load developing on the plant has the same effect; new flowers and fruitlets can be sacrificed in favor of the rapidly developing, larger fruit already present. In certain crops, a lack of pollination could be the cause of flower and, more commonly, fruitlet drop.


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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.

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