Water Quality Issues and How to Deal with Them

By Lynette Morgan
Published: September 9, 2020
Key Takeaways

If your water is not right your plants won’t reach their full potential. Dr. Lynette Morgan takes you through everything you need to know about your water supply in order to give your grow its best chance.

‘Water worries’ don’t always get much consideration from new growers as they enthusiastically set up their first hydroponic system. After all, water from the tap, which is sparkling clear and safe to drink, must be fine for plants as well, right?


Many believe this to be the case, but in fact it’s often treated municipal water that causes the most problems for hydroponic growers and many gardeners might not even be aware of the problem.

Pure water is actually a rather rare occurrence—the water we drink and irrigate our plants with is not usually just H2O, but a solution containing a wide range of minerals, dissolved gases, organic matter, pathogens, dust and chemicals.


Many common substances dissolved in or carried by water are harmless to plants, such as the calcium and magnesium present in hard water sources. Other contaminants, however—which might not pose any problems at all in human drinking water—can create havoc in a carefully balanced hydroponic system and with sensitive plants.

Read also: The Top 7 Mistakes Made By Hydroponic Growers

How Do We Find Out About Our Water?

Fortunately, most water worries are relatively easy to treat with a little knowledge and some modern technology. Knowing exactly what you are dealing with is vitally important, however, as some water treatment options can be more toxic to plants than the water issue being treated.


A water analysis or report is always the best place to start if water quality issues are suspected—municipal water suppliers should be able to provide customers with a full water report, which will include a mineral analysis as well as listing water treatment additives that could be present, such as chlorine or other chemicals.

For those using other water supplies—such as groundwater, river or dam water—obtaining a water analysis is relatively easy and all that is required is to send a sample off to a testing lab. While extremely useful, water reports might not cover all your potential problems—but they’ll usually give you a fairly good indication of where any major issues lie with your water supply.


Read also: Hydroponic Lab Analysis Tests and How to Use Them

Water Quality Issue Number One: Hard Water and High Alkalinity

This is probably the most common water quality issue dealt with by hydroponic growers worldwide, even those using treated city water. Groundwater might be ‘hard’, as water from rivers, dams and city water supplies can be, although rainwater in unpolluted areas is usually considered low-mineral or ‘soft.’

Municipal water supplies across the country range from very hard to soft, depending on where the individual city water supply is taken from. Hard water has a high mineral content, usually originating from magnesium, calcium carbonate, bicarbonate or calcium sulfate, which can cause hard white lime scale to build up on surfaces and growing equipment.

Hard water might also have high alkalinity and pH levels, meaning that lots of acid is required to lower the pH in hydroponic systems to ideal levels and maintain it there. A high alkalinity level would be considered to be greater than 10 ounces per quart of calcium carbonate and a low alkalinity level less then 100 milligrams per quart.

While hard water sources do contain useful minerals—Ca and Mg mostly—they can upset the balance of the nutrient solution and make other ions less available for plant uptake. Large-scale commercial growers can counter these problems by adjusting their nutrient formulations to take the levels of calcium and magnesium into account and by pre-acidifying hard water before it is used to make up nutrient solutions or to top up reservoirs.

The acid used for this purpose is usually either nitric or phosphoric or a 50/50 mixture of the two, the reason being that acids add minerals to the water or nutrient solution and the combination of N and P from these acids can be adjusted for in the nutrient formulation as both are taken up by plants at relatively high levels. This pre-acidification of the water means that less acid is then required in the system to keep the pH down to optimal levels.

Read also: Hard Water or Soft Water: Does My Garden Care?

Smaller-scale growers also have the option of using one of the many excellent hard-water nutrient products on the market. These hard-water nutrients are specifically designed to deal with the effect of hard and alkaline water on pH levels and usually incorporate the ammonium form of nitrogen (NH4) to keep pH levels down.

Hard water formulations also assist in keeping macronutrients in balance when using a water source that already contains levels of plant-usable elements such as calcium and magnesium. Some growers have made the mistake of using household water softening units to deal with the problem of a hard water source.

Unfortunately, while these are fine for softening water for drinking and home use, they usually incorporate a process that adds sodium chloride to the water. Sodium is an issue for hydroponic systems and is an unwanted element with the potential to cause plant damage, so use of these water softeners for hydroponic water supplies should be avoided.

Water Quality Issue Number Two: Unwanted Minerals, Sodium

Water supplies will all carry some mineral content unless the water has been through a distillation or reverse osmosis process to remove it. Groundwater and city water tend to be highest in mineral content—as the minerals leach from the surrounding soil into the water—and rainwater the lowest. The most commonly occurring minerals in water supplies are calcium and magnesium, which are not problematic for hydroponics provided they are not present at excessively high levels.

Other common elements are sodium and trace minerals, which can occur at varying levels in different water supplies. Sodium levels in excess of 2,000 ppm have been found in some inland well water in arid regions, although most well water sources don’t pose such an extreme problem.

Sodium contamination usually occurs from common salt—sodium chloride—which is present to varying degrees in most soils and might also be present from salty sea spray, salt water penetration of wells or from sources deliberately added during water softening processes.

Read also: Understanding and Using NFT Hydroponic Systems

Sodium is not taken up by plants to any large degree, so it can end up accumulating in hydroponic systems (more so in recirculating systems) and displacing other elements. Trace elements in water supplies, such as copper, boron, zinc and iron, might also sometimes occur at high levels.

While lower levels of trace elements can be adjusted for in nutrient formulations, higher levels often need reverse osmosis treatment or dilution with a lower-mineral water source to keep these minerals below toxic levels. Some hydroponic crops such as tomatoes are far more tolerant of high levels of sodium than other more sensitive crops like lettuce, so this can be taken into account when deciding whether or not a salty water source needs treatment. For moderate levels of sodium, growers can opt to avoid recirculating the nutrient, thus preventing sodium or other unwanted elements accumulating over time. In this case avoiding recirculating systems such as NFT set-ups in favor of media-based drain to waste-type set-ups is often enough to avoid excessive sodium buildup.

Water Quality Issue Number Three: Water Treatment Chemicals

Many city water sources are perfectly acceptable for soilless growers and hydroponic systems and can be used with no adjustment or treatment. However, water treatment options used by city water suppliers change over time and with advancing technology. In the past the main concern was chlorine in city water supplies.

Chlorine is a disinfecting agent that destroys bacteria and human pathogens and residual chlorine can usually be detected by smell in a water source. High levels of chlorine can be toxic to sensitive plants—although chlorine is a chemical that rapidly dissipates into the air and it can easily be removed by aerating the water or just letting the water sit or age for a few days before use.

While chlorination of water supplies was relatively easy for hydro growers to deal with, city water treatment plants are now moving more frequently toward the use of other methods for treating drinking water.

Scientists discovered that some human pathogens are resistant to chlorine, so water safety regulations had to change and alternative disinfection methods came into more frequent use. These days water might still be chlorinated, but an increasing number of city water suppliers have switched to the use of ozone, UV light, chloramines and chlorine dioxide as methods of treatment.

Read also: Tap Water and its Impact on Hydroponic Nutrients and Supplements

While many of these methods are not a problem for hydroponic and soilless growers, the use of chloramines and other chemicals by many city water treatment plants can pose a problem for plant life where high levels are regularly introduced into water supplies.

Chloramines are much more persistent than chlorine and take a lot longer to dissipate from treated water, which means they can build up in hydroponic systems and cause plant damage.

This damage is very difficult to diagnose, as it looks similar to many root rot pathogens and growers aren’t usually aware of what is actually causing the problem. Some plants are also naturally much more sensitive to chloramines than others, so determining levels of toxicity has been difficult.

Hydroponic growers who have concerns about the use of chloramines in their city water supply can treat their water with specifically designed activated carbon filters or by using dechloraminating chemical or water conditioners, which are sold by the aquarium trade to treat the water in fish tanks.

The chloramine carbon filters must be of the correct type, with a high-quality granular activated carbon that allows for the long contact time required for chloramine removal.

Growing systems that utilize substrates such as coco are a safer option than soilless culture or recirculating systems when water treatment chemicals are suspected to be a problem—these natural substrates provide a buffering capacity much like soil does and can deactivate some of the treatment chemicals contained in the water supply.

Water Quality Issue Number Four: Grubby Water and Pathogens

Generally, city water supplies are filtered to remove organic matter and treated to kill any microbial life, which includes human and plant pathogens. However, other water sources like wells, rivers, dams and rainwater can harbor both organic matter and potentially damaging plant pathogen spores.

Many large commercial hydroponic operations use untreated water sources with few problems, but in some areas pathogen contamination can be an issue. Zoosporic pathogenic fungi such as Pythium and bacteria can survive and be distributed in water, although these can be relatively easily cleaned up by the grower before they can pose any threat.

Read also: Understanding Pythium Root Rot

The safest options are UV, ozone and slow sand filtration, as these won’t leave chemical residues, which could harm young sensitive root systems. Small UV treatment and filtration systems such as those used in fish ponds and aquariums are suitable for treating water for hydroponic use and will kill plant pathogens and algae. These are best used for treating water only—not nutrient solutions—as UV radiation can make some nutrients unavailable for plant uptake.

While it is possible to treat water sources with chemicals such as bleach (chlorine) or hydrogen peroxide (H2O2), this can be a risky process. Levels of these sanitizer chemicals high enough to kill plant pathogens will certainly damage young or sensitive plants unless the chemicals are deactivated or removed before being used to make up a hydroponic nutrient solution.

H2O2 is deactivated when it reacts with organic matter in the water and chlorine will dissipate over time, particularly if the water is aerated, but determining when these active chemicals have reached levels low enough to be safe for plants is difficult.

There are test strips sold through aquarium suppliers that might help, but it’s usually an easier option to rely on safer methods of water treatment for pathogen control.

Good-quality water is vital to the success of any hydroponic system and growers today have a wide range of tools to assess their own water supply and carry out any treatment that is required. Investing in high-quality water is an essential step in any new hydroponic setup and will help prevent any number of serious problems down the road.


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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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