Cloudy Hydroponics Water? A Quick Guide For Remedies

Hydroponics is a controlled process wherein every factor is controlled with such precision to ensure that optimal plant growth and development. A common problem for beginners and even some veterans is when their water turns worryingly cloudy!

The main reasons for cloudy hydroponics water are dirt and debris, abnormal nutrient levels, root rot, and microorganism growth. The simple and recommended solution is to flush, sanitize, and sterilize the system by using diluted chlorine bleach or diluted hydrogen peroxide (H2O2).

Cloudy water can be a cause for alarm because it may be a symptom for more serious complications. We’ll run through the best course of action and explain the possible causes.

The 4 Main Reasons for Cloudy Hydroponics Water

There are several reasons why water in hydroponics may turn cloudy. It could be due to regular old dirt, root rot, bacterial growth, or nutrient turbidity. We’ll tackle these one by one, explaining the negative effects and the possible remedies.

1- Root Rot

A perennial problem in both soil and soilless cultivation, root rot has frustrated growers for the longest time. This is either caused by overwatered conditions or due to fungi. In hydroponics, water mold genus Phytophthora.

In effect, this leads to poor plant growth, discoloration in the leaves, and true to its name, black and decaying root systems.

Decaying root matter along with mold dispersed in the water is one of the most common causes of cloudy water in hydroponics.


Food grade hydrogen peroxide can be applied on a running system 1.7-2ml/L to treat root rot. For direct application, a food grade hydrogen peroxide solution composed of 2 parts water and 1 part hydrogen peroxide will prove effective. Let it sit for 15 minutes.

Chlorine bleach in the amounts of 4-10 drops per 1 liter of water (4-10 drps/L) is recommended in treating root rot. Run the diluted bleach solution over the infected root system and let it sit for 15 minutes.

Reasons hydroponic water – Infographic

2 – Microorganism Growth

Microorganism growth is another main cause of cloudy water. Microorganisms can live suspended in the water but often they manifest in the form of biofilm. Microorganism growth can negatively affect plant growth in hydroponics because they compete with the plants for the oxygen and nutrients present in the water.

Their presence can result in phytopathogen infections in plants. Thick biofilm accumulation will cause clogging and nutrient competition which will make water circulation and nutrient distribution less effective, respectively.


To remove thick biofilm accumulation in hydroponic it is necessary to have periodical flushing, sanitization, and sterilization of the entire system by scrubbing it clean with a diluted solution of around 9.7g/L for powdered bleach and 10ml/L for liquid bleach.

As a preventive measure and as stated before, food-grade hydrogen peroxide (H2O2) can be incorporated in the reservoir of a running hydroponic system at a ratio of 2-5ml/L every 4-5 days. Water treated with hydrogen peroxide should be circulated in the system for 30 minute before every nutrient change.

Another preventive measure is to make sure all surfaces in a system are lightproof. Painting a hydroponic system such as the pipes and reservoir can prevent sunlight from penetrating the water in the system thereby preventing microorganism growth.

3 – Abnormal Nutrient Levels

Nutrients are necessary, however too much nutrients will cause the water to turn cloudy. This problem is more apparent when using organic nutrients instead of inorganic nutrients.

Abnormal levels of electrical conductivity (EC), acidity (pH), and parts-per-million (ppm) may cause cloudiness. The optimal levels are 1.2-2 for EC and 5.5-6.5 for pH. Optimal ppm is dependent on the system size and plant type.

Increased levels of EC and ppm will cause an overabundance of nutrients which may cause nutrient burn as evidenced by yellow/brown leaf edges and the curling of leaves.

Elevated pH levels can cause the water to become too basic which will hinder nutrient uptake. This will lead to growth deficiencies.


To normalize EC and ppm levels, it is only necessary to add fresh water in the system.

To normalize pH levels, baking soda or vinegar can be added to increase or decrease the pH levels.

4 – Dirt and Debris

Dirt and debris suspended in water can give the appearance of cloudiness.

Dirt and debris can be introduced externally due to wind, outdoor elements, or negligent care. It’s also possible that dirt and debris can be caused by loose growing mediums that fall from the net pots or grow tray and settle in the reservoir.

This is further exacerbated when there is an air pump in the system which prevents the dirt and debris from settling at the bottom.

Though not necessarily an urgent problem, it is possible that pathogens may be in the dirt and debris, hence it’s recommended that they be removed. Likewise, dirt and debris can cause clogging in the system.


Again, flushing, sterilizing, and sanitizing the system using either bleach or hydrogen peroxide in the prescribed formula will be effective in removing dirt or debris.

The Simple and Recommended Solution

In almost every instance wherein water in hydroponics is cloudy, the safest and most recommended course of action is to flush, sanitize, and sterilize the entire system with either diluted chlorine bleach or diluted hydrogen peroxide (H2O2).

Microorganisms are killed when strong oxidizing agents are applied which cause the bacterial cell membranes to deteriorate while the excess of nutrients are entirely removed and replaced.

Hydrogen Peroxide (H2O2)

H2O2 is a milder cleaning substance and can be used in running hydroponics systems, effectively eliminating microorganisms in the water. It is recommended that food-grade hydrogen peroxide is used.

Food-grade hydrogen peroxide (35%) can be incorporated in the reservoir of a running hydroponic system at a ratio of 2-5ml/L every 4-5 days. Likewise, water treated with hydrogen peroxide should be circulated in the system for 30 minute before every nutrient change.

Chlorine Bleach

Generally, chlorine bleach, a much stronger cleaning substance, can only be used on an empty system. Diluted chlorine bleach can be used to effectively sterilize and sanitize an empty hydroponics

A diluted chlorine bleach solution of 9.72g/L for powdered bleach and 10ml/L for liquid bleach is recommended. This substance or solution cannot be used on a running system.

We have a guide on how to use diluted bleach to periodically clean your system and to treat root rot.

What about Beneficial Microorganisms?

Of course there are beneficial microorganisms which are positive to growth and development, providing a symbiotic relationship to the growing plant. They can be found in the water or more commonly in the roots of the plants.

These beneficial microorganisms include pseudomonas putida, trichoderma atroviride, and rhizosphere bacteria, among others. These improve root health and crop success in both soil and soilless cultivation.

The problem is that most hydroponic growers aim for a sterile system to narrow down the factors they need to monitor and take into account. The goal of a sterile system is to ensure that only the essentials are present for the sole consumption of the plants – nutrients, water, oxygen, and carbon dioxide.

The introduction of microorganisms, be it beneficial or harmful, may cause disruption to this tenuous balance because of how they interplay with the rest of the system. For example, there might be competition over the nutrient uptake in the water or there is not enough dissolved oxygen in the reservoir because of the increased presence of microorganisms.


  1. Cloudy hydroponics water can be caused by dirt and debris, abnormal nutrient levels, root rot, and microorganism growth.
  2. The simple and recommended solution is to flush, sanitize, and sterilize the entire system either with bleach or hydrogen peroxide.
  3. The aim of most hydroponic growers is a sterile system to narrow down the factors to monitor and to ensure everything in the system is directed towards the plant’s consumption of what the hydroponics system has to offer. is part of the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites like mine to earn advertising fees by promoting good quality products. I may receive a small commission when you buy through links on my website.



A young Italian guy with a passion for growing edible herbs. After moving to the UK 6 years ago in a tiny flat, it was impossible to grow herbs outside. So I start my journey in growing indoor and so I decided to share my knowledge.

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