What’s the Problem? Hydroponic Troubleshooting

By Lynette Morgan
Published: March 6, 2020 | Last updated: April 30, 2021 01:16:54
Key Takeaways

Troubleshooting can be difficult when coming across something strange, not quite right, or downright destructive in a previously healthy hydroponic system.

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Most of the problems we encounter in a hydroponic garden are relatively easy to diagnose—small, visible, chewing, rasping, sucking and gnawing insect pests or furry, fluffy molds and mildews can usually be quickly identified and controlled with ruthless efficiently.


However, what frustrates many novice and experienced hydroponic gardeners alike is coming across something strange, not quite right or downright destructive in a previously healthy crop. Troubleshooting such occurrences can be difficult, as there could potentially be multiple causes for the same set of symptoms or, in particularly unlucky cases, more than one problem can exist at the same time.

Hydroponic troubleshooting skills generally improve with time and experience and while newer growers may be baffled by something as simple as a mite infestation, the more advanced hydroponic gardener can still be taken by surprise by strange and unusual plant symptoms. Here are some common problems whose cause may be a little mysterious at first.


Humidity Disorders

Humidity is an environmental factor that frequently needs troubleshooting. Low humidity may result in leaf burn if the plants cannot take up water fast enough to replace what is lost through transpiration. High humidity can cause a range of other issues, the most common being a predisposition to fungal disease outbreaks.

High humidity is also involved in some more complex physiological disorders, including glassiness, oedema, tip burn, and blossom end rot. Water-soaked, almost-translucent patches on the leaves of often young plants is called glassiness and is typically seen first thing in the morning, with these patches drying up later in the day.

Read also: Physiological Disorders of Indoor Gardens


Glassiness is caused by high humidity combined with root pressure, which may also show as guttation or droplets forming on the tips of leaves in the early morning. During the cooler night conditions, roots pump up excess moisture to the foliage, where high humidity levels prevent the plant from ridding itself of the water via transpiration. As a result, the leaf tissue becomes water soaked. Increasing air flow and additional heating usually help prevent this disorder.

Tip burn in lettuce, strawberries and many salad green crops, and blossom end rot of tomatoes and peppers, are disorders caused by a lack of calcium transport within the plant out to the leaf tips or ends of fruit.


When humidity is high, transpiration is reduced. So while there is usually more than sufficient calcium in the nutrient solution, the plant is unable to transport it up to the developing plant tissue in leaf tips and fruitlets, and this tissue breaks down and blossom end rot or tip burn occurs. Lowering humidity—the ideal relative humidity for most crops being 70 to 75%—and increasing air flow over the foliage helps plants transpire and move calcium out to the tissues prone to these disorders.

Gaseous Issues: Carbon Dioxide (CO2), Ethylene, and Sulphur Dioxide

Two less common, but potentially serious, problems in indoor gardens arise from gases. Carbon dioxide (CO2) enrichment is a useful way of boosting plant growth and development, but overdoing the CO2 doesn’t result in ever-increasing yields. Optimal carbon dioxide enrichment levels for most plants are in the 600 to 1,200 parts per million (ppm) range. The ideal dose depends on a number of factors such as plant maturity, previous exposure to CO2 and species.

The most common cause of CO2 toxicity in an indoor garden is broken or inaccurate CO2 monitoring equipment. Many growers are not even aware that CO2 damage can occur. This can become toxic for humans, too—in the 5,000 ppm range, side effects include dizziness and lack of co-ordination.

The first signs of CO2 toxicity are often mistaken for other problems and include leaf damage such as chlorosis (yellowing), necrosis (especially on tomatoes and cucumbers) and curling of leaves. Sometimes growth reductions and stunting caused by high CO2 levels can occur with no other visible damage symptoms or injuries to the plants. Correct maintenance of CO2 monitoring equipment, including using backup testing methods, are advisable if CO2 is used indoors.

Read also: The Symbiotic Relationship Between CO2 and Ventilation

The second gaseous issue—where CO2 enrichment is occurring via the burning of certain fuels—is more common. In this case, plant-damaging by-products such as ethylene or sulphur dioxide can be generated, which cause plant injury and even crop loss when incomplete combustion of the fuel has occurred.

Ethylene (also given off by many ripening fruits and vegetables) is a plant hormone that causes fruit and flower drop as well as leaf twisting and distortion at levels as low as 0.05 ppm. Use of clean sources of CO2 and a good level of ventilation help prevent ethylene-induced growth problems.

Spray Damage from Pest Control Products

While pest and disease-controlling products are often essential in most hydroponic gardens, these compounds can lead to some misinterpreted damage. Spray damage on plants grown indoors is far more common than most of us realize and symptoms are often attributed to another source.

Anything sprayed onto plant foliage—even water—has the potential to cause leaf damage depending on factors such as environmental conditions, plant health, thickness of leaf cuticle, stage of growth and formulation of the spray product. Overuse of soap/oil sprays for insect control is one concern—these may seem like harmless compounds, but they have the potential to severely damage leaves and repeated sprays are known to almost defoliate crops under certain conditions.

When using any spray compound, particularly soap/oil sprays, I recommend trying the product on a few leaves first, waiting two or three days and checking for damage before spraying all plants. Also, avoid using these sprays repeatedly, particularly on young or sensitive plants.

Spray damage symptoms usually appear within 24 hours of spraying and show up as dark markings on foliage, which may later turn brown and dry up. When troubleshooting any new or strange foliage spots and marks, it’s always a good idea to recall what may have been sprayed on the plants in the previous few days or keep a journal of products used, the rate and date of application.

Super Bugs and Resistance

Another increasingly common problem related to the use of pest and disease-controlling sprays is the development of super bugs and resistant diseases.

Gardeners may start to notice a particular spray or compound they have always used to kill insect pests and control diseases no longer seems effective and an explosion in pest populations has resulted. Many of the spray compounds we use for plant protection should not be applied more than two or three times over an entire growing season.

Read also: The Do's and Don'ts of Foliar Feeding

Repeated applications of the same class of control compound can result in the insects and diseases building up genetic resistance to that compound, and eventually the spray product stops controlling the problem and a new strain of super bug has developed.

Many of the once highly effective pesticide and fungicide compounds have been overused to the point where they no longer provide any control at all, leaving growers frustrated that they can no longer kill a simple pest such as whitefly or tackle an outbreak of powdery mildew.

The solution is to rotate a range of control options when dealing with pest and disease outbreaks and include environmental control, integrated pest management, biological controls, traps and resistant cultivars.

Chemical Issues

Some plants we grow hydroponically are more prone to certain water and nutrient quality issues than others. While tomatoes are extremely tolerant of sodium, high EC and water treatment chemicals, cucumbers are very susceptible and far more likely to show troublesome symptoms.

The cucumber halo is a yellow band around the edge of the leaves that shows up rapidly in response to chloride or a buildup of other treatment chemicals coming in through the water supply (usually city water). It can also be caused by high salts in the grow medium or high EC.

Certain treatment chemicals in city water can cause problems for sensitive plants such as lettuce, strawberries and cucumbers, and also with young seedlings. Symptoms may include leaf discoloration, wilting, stunting and root die-back.

Read also: Understanding Reverse Osmosis and How It Benefits Plants

This problem can be difficult to differentiate from similar symptoms that have other causes. If a water supply is suspected of causing growth issues, a quick test can be run by growing seedlings of a sensitive species with both the suspect water supply and distilled, reverse osmosis water or rainwater to determine if any differences occur.

Strange Plant Problems

One of the strangest issues encountered by gardeners, particularly those who specialize in tomatoes, may be discovered when cutting open a fresh fruit. A mass of germinated seeds inside the tomato fruit tissue can look rather alarming.

This premature germination of tomato seeds while still enclosed in the fruit is termed vivipary and it may also be found in tomatoes bought from the supermarket that haven’t been stored correctly. Viviparous germination occurs when the natural germination inhibitors surrounding the seed break down, allowing the seeds to germinate inside the moist environment of the fruit.

This mostly occurs in fruit that experience cold temperatures during development or storage—tomatoes should never be stored in the refrigerator—as well as the usage of gibberellic acid for fruit set or ethylene for fruit ripening.

Another strange symptom commonly found in hydroponic tomatoes is the formation of masses of hard bumps or root initials on the plant stem, often accompanied by stem splitting where these emerge. Tomato plants can produce large numbers of these adventitious roots anywhere on the stem and this is usually in response to wounding, disease, root die-back or hormone contamination, but it can also occur on perfectly healthy plants during times of rapid growth and development.

Novice growers often find the development of roots high up on their tomato plant stems a little alarming and may attribute it to disease or genetic deformity, but this condition is usually not a problem unless there is an underlying poor growth and development issue.

Unseen Pests

Usually insect pests are relatively easy to spot, catch and squash, but some are so small that their presence and damage is often overlooked. The most common pests in this category are mites, which are frequent inhabitants of dry and protected indoor gardens. Mites are difficult to see—those with good eyesight may be able to make out tiny orange dots on the undersides of leaves when a heavy infestation is present.

They also produce leaf bronzing, or silvering—an overall dullness to the leaf surface and fine webbing on the undersides of foliage. If left uncontrolled, a severe mite infestation will destroy plants over time. Mites are best controlled with a mixture of sprays and environmental modification. They thrive in dry, low-humidity conditions, so increasing humidity levels helps restrict their population growth.

Read also: Nematodes: Allies or Enemies?

Parasitic nematodes, also called eel worm or needle worms, are another pest invisible to the naked eye. Parasitic nematodes can only be seen under a microscope, but they cause distinctive damage to roots, including root knots, swellings, galls, stunting, root death and overall loss of vigor in the plants.

Nematode species infecting hydroponic crops include the lesion, needle and root knot nematode species. Apart from root symptoms, these worms can also transmit a number of plant viruses. Nematodes usually find their way into a hydroponic system via contaminated soil, through seedlings or transplants or in water sourced from dams, wells and streams. Fungus gnat adults and larvae can also carry nematodes.

A grower with a heavy nematode infestation that causes severe root damage on plants needs to have the system shut down and cleaned with sterilization agents, as these pests are difficult to control using other methods.


Troubleshooting the sudden onset of a new and confusing problem in a hydroponic garden can seem a little daunting, but careful observation and understanding the basics of plant growth and development can help growers search for potential answers. Asking more experienced growers or retail shop employees are also good places to start, as many will have already tackled problems in their own gardens.


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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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