7 Causes of Bad-Smelling Hydroponics Water (and Solutions)

No one would like hydroponic water that smells foul—that’s for certain. Frankly speaking, I would not eat anything from a hydroponic garden that smells weird! But, believe it or not, I have encountered this issue numerous times in the past and have investigated several potential causes.

In general, unpleasant odor in hydroponic water is caused by root rot, lack of oxygen in the nutrient water, hot water temperature, algae infestation, too much organic material, a low pH, and uncleanliness. To avoid this, maintain clean nutrient water with high oxygen levels, cool temperature, and neutral pH, and keep it away from direct sunlight.

I know one of the words running in your mind right now is sanitation. Sanitation is the key—you may be thinking. But how does this term differ from sterilization? You will find out at the end of this article, so let’s go!

1. Hydroponic Root Rot

The plant disease called root rot is the most common cause of foul smells in hydroponic water. It occurs as a result of poor management practices regarding oxygen supply in the hydroponic system, water temperature, pH, and even cleanliness. Fungi and oomycetes, the primary causes of root rot, reproduce under adverse conditions.

Let me tell you a secret. Root rot cannot thrive in a well-oxygenated environment. That is their weakness!

Solution: Do not completely immerse the roots!

This strategy works best in passive deep water culture systems. Submerging your roots up to the top will drown your plant. When this occurs, the roots become weakened due to low oxygen levels and begin to rot, resulting in a foul odor!

Hydroponic root rot: prevention, detection, elimination (2020)

2. Oxygen Shortage in Hydroponic Water

Lack of oxygen in the hydroponic water can result in an unpleasant reservoir smell. This environment promotes the growth of Pythium spp., which is an organism that causes root rot disease.

Solution: Use air pumps to generate bubbles and increase dissolved oxygen levels.

Dissolved oxygen is basically the amount of oxygen found in water. It may seem too complicated, but it is not some premium version of oxygen! So, in aquatic systems, dissolved oxygen is what allows fish to keep breathing!

In hydroponics, air pumps generate bubbles that promote gas exchange. These bubbles allow oxygen to enter and carbon dioxide to exit the water’s surface. Higher dissolved oxygen levels enable the roots to perform their function of delivering nutrients and water to the plant.

   Discover more in our article on too many bubbles! 

Without stagnancy, the roots interact with every component of the hydroponic setup in a systematic manner, and the organism that causes root rotting cannot proliferate.

3. Hot Water Temperature

Microorganisms such as fungi, bacteria, and algae thrive in hot hydroponic solutions. When they proliferate in water, all of these contribute to the production of foul odors.

Hot nutrient water is a favorable condition for the reproduction of microorganisms that can adversely affect your hydroponic veggies and herbs.

Solution: Coat the reservoir in white paint or use reflective insulators to keep the water temperature stable.

You might be curious why white? Objects of white color reflect light, therefore, hydroponic tanks with a white coating will not retain either heat or light.

Styrofoam boxes are another awesome container choice for a hydroponic reservoir since they are white and act as an insulator.

Reflective insulators of this kind from Amazon are also great choices. They hinder heat absorption by your hydroponic system and reduce radiant heat gain!

Pro Tip: Install thermometers in various locations throughout your growing room to track temperature.

Solution: Use a water chiller. If you are on a tight budget, you can add ice packs or cold water every 15 minutes until the optimum nutrient solution temperature of 65 to 80°F.

   Explore more on this in our article about water chillers.  

4. Algae Infestation

Algae are organisms that can release a musty and/or rotting odor. Slimy roots are also a manifestation of algae. Combating algae entails hindering the entry of sunlight into the hydroponic system’s nutrient water reservoir.

Solution: Monitor water temperature and sunlight exposure and entry.

An interplay of solar radiation, hot water temperature, and nutrients promotes the growth of algae; therefore, wrap every possible point of entry so that sunlight does not reach your nutrient water.

Preventing Algae Infestation
Preventing Algae Infestation

This can be accomplished by using an opaque nutrient water tank and tubing. Another way to prevent sunlight entry is by covering the exposed growing medium with perlite, pebbles, dark paper, or black cloth.

5. Too Much Organic Material

A rotting smell in hydroponic water might be from the abundance of organic materials, namely growing mediums, in the hydroponic system.

Let me ask you a question. Which of the following will decompose first? a) gravel, b) coconut husks, or c) perlite?

If you answered coconut husks, then you are right.

Remember that the process of decomposition involves bacteria and fungi to degrade the material. Hence, another key point that I want you to note is that a moist environment is a good place for these organisms to grow and reproduce.

Thus, if you observe a foul smell in your hydroponic garden, it might be your growing medium! Organic growing mediums such as coco coir, peat moss, and vermicast are potential sources of bad odor.

Solution: Shift to inorganic growing mediums such as perlite, vermiculite, and clay pebbles.

But before shifting, you can try changing your growing medium with a fresh batch again. If the unpleasant odor is still observed, then consider shifting to media that do not degrade.

6. Low Nutrient Water pH

Most acidic solutions have a rotten egg smell. This can also be observed in hydroponics once the nutrient water reaches low pH levels.

Solution: To correct this, one can use pH neutralizers or pH up solutions.

Low pH in nutrient water promotes the growth and reproduction of bacteria and fungi. These harmful microorganisms can cause damage to the plant roots such as root rot. When root rot is favored, a foul smell can be observed.

Monitoring pH to Avoid Foul Odor
Monitoring pH to Avoid Foul Odor

What You Can Do: Check the pH every 2-3 days. The optimal solution pH for hydroponic systems is generally between 5.5 and 6.8.

Pro Tip: You can buy pH-up products, like this one on Amazon, which can be used to adjust the pH of hydroponic solutions. But if you are on a limited budget, baking soda is also effective in increasing pH.

7. Unclean Hydroponic System

Overall, poor sanitation of the hydroponic system is another cause of a smelly growing site. This includes all the system equipment and water odor.

Solution 1: Change the water in your hydroponic system every 2-3 weeks.

Another useful strategy is to replenish your water reservoir with water when it evaporates. This is called topping up.

   Read our article on how often to change hydroponic water for more information on topping up. 

Solution 2: Disinfect by circulating food-grade hydrogen peroxide.

If algae infestation is already really bad—they are already in hard-to-reach areas in your hydroponics—disinfecting using food-safe hydrogen peroxide is the best course of action!

To do this, allow 3 mL of food-grade hydrogen peroxide to flow and circulate in your system for every gallon of nutrient water. This can be added once a week to mitigate algae infestation without harming plant roots.

Another advantage of doing so is that food-grade hydrogen peroxide will oxygenate the roots of your plants.

Solution 3: Do system cleaning.

Follow the steps below to properly clean the hydroponic system.

  1. Remove the net pot or cup containing your plants with care.
  2. Disassemble all movable parts of your system
  3. Rinse-scrub-rinse with a soft cleaning brush and a gallon of water containing 1.3 oz unscented bleach.
  4. Dry out all parts completely before starting the cycle again.
  5. Use a fresh nutrient water mix as well!

Solution 4: Use carbon filters.

Carbon filters can be used in your growing location to absorb all the odor from the air. This is practical most especially if you notice a continuous bad odor in your garden.

However, before investing in this additional equipment, try the aforementioned solutions first. If the foul odor prevails, then I suggest purchasing carbon filters like the one below on Amazon.

Sanitation vs Sterilization

Sanitation only reduces the number of microorganisms in an object, whereas sterilization uses strong chemicals to completely remove the harmful microorganisms. Both can be practiced to ensure the cleanliness of the entire hydroponic system.

To demonstrate the distinction, sanitation is the act of washing your utensils after eating with dishwashing liquid and a sponge. Why? Because doing so reduces the number of microorganisms present to a safe level.

If you soak your utensils in 95% or 70% ethyl alcohol, you are sterilizing them. Because this process will kill any bacteria that may be present in your utensils.

When you wipe plant debris, dust, and soil from the reservoir of your hydroponic system, you are sanitizing it. On the other hand, you are sterilizing when you use bleach or food-grade hydrogen peroxide to scrub away dirt during system cleaning.


How do I know if I have root rot in my hydroponic system?

Root rot is easily identified by dark brownish, mushy roots. If the water smells bad (like a swamp) or is slightly sulfurous, it’s another sign that you’re dealing with rot. You can also observe the curling and yellowing of a plant’s leaves.

Can I reuse hydroponic water?

Some gardeners reuse hydroponic water, but this is not recommended. Excess minerals and salts in hydroponic water may accumulate during the next growing cycle. Plant disease is another risk factor. The previous growing cycle may have developed a pathogen that can be transferred in the next cycle.

Can you have too much oxygen in hydroponics?

Yes, one can have too much oxygen and too many bubbles from air pumps which is dangerous for plants. Overoxygenation can raise the temperature of the water, disintegrate hydroponic nutrients, and produce an acidic solution. Learn more about this in our article about too many bubbles in DWC hydroponics.


Foul smell in hydroponics can be caused by hydroponic root rot, lack of oxygen in the nutrient water, hot water temperature, algae infestation, too much organic material, low pH, and unclean hydroponic system.

To prevent bad hydroponic water odor, it is essential to oxygenate the water, keep the temperature of the nutrient water stable at 65 to 80°F, avoid direct sunlight exposure, use inorganic growing mediums, monitor water pH, and maintain the cleanliness of the hydroponic system.


  • “First Report of Root Rot of Hydroponically Grown Lettuce Caused by Pythium myriotylum in a Commercial Production Facility” by Stanghellini ME, Kim DH, Rakocy J, Gloger K, Klinton H. in Plant Diseases
  • “Indicators: Dissolved Oxygen” by National Aquatic Resource Surveys in the United States Environmental Protection Agency
  • “How to Sanitize and Sterilize Hydroponic Systems” by Godfrey, M. in Upstart University
  • “Understanding Root Rot Disease in Agricultural Crops” by Williamson-Benavides, B.A. and Dhingra, A. in Horticulturae 2021
  • “Understanding the Difference Between Cleaning, Sanitizing & Sterilizing” by N/A in Canadian Institute of Food Safety

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