Unpleasant Odor In A Hydroponic System (And How I Solve It)

We know that you don’t want this foul odor to spread in your garden or even in the other areas of your house. Don’t worry, because this article will help you. We will reveal to you the ways of minimizing unpleasant smells in your indoor hydroponic system. Before we proceed to the solution, let us first dive into the causes of foul odor in your hydroponic garden.  

What causes a bad smell in hydroponic system?

Knowing what causes the foul odor in your hydroponic garden is essential to determining the best solutions. The following are some factors that can cause an unpleasant smell in your growing room.  


In hydroponic gardening, the plant roots can have direct contact with organic materials. It can result in the growth of bacteria and may spread in your home.

Using a high amount of organic material like coconut fiber in your garden can cause a bad smell.  


Another cause of smelly hydroponics is microbes. Bacteria may come into a microbe form, a specific bacterium that carries diseases. It causes an unpleasant smell in the hydroponic water by throwing off oxygen and pH levels.  

Insufficient oxygen in the water 

Not enough oxygen in the water can also lead to a foul odor in your garden.  

Poor maintenance

Your hydroponic garden may smell like rotten eggs due to poor maintenance.  

Controlled temperatures

Controlled temperatures in the closed system also contribute to the unwanted smell.  

Poor sanitation

Poor sanitation can also lead to an unpleasant odor in your garden. Remember that proper sanitation is essential for the health of your plants and your system. With that, you need to be responsible for practicing good sanitation. Dispose of plant waste properly, sterilize and clean your tools and containers. Make sure to keep floors dry and clean. You can also sterilize and clean the system equipment. By applying proper sanitation, you can also avoid plant disease.  

pH levels problem 

PH levels can also cause a bad smell since it causes plants to lose growth and color.  

Solutions to reduce the foul smell in hydroponic garden

Now that you have learned the possible causes of bad smells in your hydroponic system, we will provide you with efficient ways to solve the odor problem in your garden.  

Change water frequently

By changing the water frequently for about two to three weeks, you can reduce or even eliminate the bad odor in your hydroponic system.  

Hydrogen peroxide

Hydrogen peroxide comes with devastating effects on microbes and organic tissues. It helps to reduce the growth or destroy viruses, bacteria, and common pests. Aside from reducing the smell of the hydroponic system, hydrogen peroxide is also beneficial for treating root rot, pre-treating seeds, pest control, and killing fungus. It also stimulates nutrient absorption and root growth. Hydrogen peroxide is also helpful in enhancing the oxygen content in water. It can boost overall plant health and growth.  

Use air pump 

With the use of an air pump, you can produce more oxygen into your hydroponic system. It is beneficial to avoid a smelly growing room.  

Use inorganic materials as a medium

Bacteria are a major cause of smelly hydroponic systems. The best thing to solve it is to use inorganic materials as the medium in your hydroponics. You can use rockwool, perlite, grown stones, and hydroton. Inorganic materials are sustainable and reusable, and easy to use.  

Check the microbial balance of your hydroponic garden

If microbes cause a bad smell, make sure to check the microbial balance of your hydroponics. Microbial species release slime, foul odor, and other undesirable problems in your hydroponics. With this, you should have a sterilized and clean water source. Then, you can add nutrients and beneficial microbes.  

Beneficial microbes work well with the plant’s roots since they promote more minerals and nutrients and fight off parasites and diseases. You can mix it with the nutrient solution to balance the pH level. Keep in mind to keep the nutrient solution oxygenated, so bringing the good microbes will work. It is a good way to keep your hydroponic system healthy.  

Carbon filter

If a temperature problem causes a bad smell, you can set up a carbon filter. It features controlled temperature settings and timers through its fans that clean the smell and release odorless air. The fans of the carbon filter kick in as the temperature gets above the recommended range and blow air at specific intervals. Carbon filters are easy to use and install. It is effective in removing the bad smell from the areas of your hydroponic system.  

Meanwhile, the wrong carbon filter can worsen your hydroponic system. So, you should choose the best carbon filter to produce the best results. In selecting a carbon filter, you can consider the following:

l The filter should come with a deep carbon red for more carbon that lasts longer.

l The carbon needs to contact air, so the airflow between the fan and carbon can match.

l The right spigot size needs to fit on the fan’s diameter snugly. If it’s too small, there will be no air that will flow from the fan into your hydroponic system.  

Reduce the use of organic materials

Another way to minimize the smell of your hydroponics is to reduce the use of organic materials for the growing support of your hydroponic plants. It is also essential to maintain pH levels in the nutrient water to prevent microbes. You can clean or replace the growing medium to eliminate unwanted organic matter. It is good to use a dark reservoir and keep it covered to keep foreign organic matter and light out.  

Keep Proper temperature 

In hydroponic gardening, the temperature is crucial to maintain plants in the water for growth. The suggested temperature for your hydroponic system is about 65 to 75 degrees Fahrenheit. If it gets too hot in your hydroponic system, the plants may secrete more organic solutions that lead to bacteria growth.  

Clean your hydroponic system 

Cleaning your hydroponic system is an effective way to remove the unpleasant odor from your hydroponic system. You can replace the nutrient water with bleach mix and water to remove the odor. Remember that water and nutrients need to purify and clean every 1 to 2 weeks.  

Use Sanitizing spray 

You can use a sanitizing spray to eliminate the smell. The spray contains glycol molecules that will attach to odor-causing compounds in the air and change their chemistry.  

Install Exhaust fan

An exhaust fan can draw air from your hydroponic system and vent it outdoors to disperse the smell. In addition, it also helps to offer a fresh and stable supply of carbon dioxide for your hydroponic plants.  

Neutralizing crystal or gel 

A jar of formulated crystals or gel in your hydroponic system attracts the VOCs (volatile organic compounds) in the air, which carry foul odors and trap them.  

Ozone air care program 

You can equip your hydroponic garden with an ozone air care program to control the odor in your system. In addition, it also helps increase enjoyment and success in your hydroponic gardening. By installing an ozone generator, you can eradicate the bad smell that can bring inconvenience to your hydroponic system. There’s nothing to worry about because an ozone generator is compact, lightweight, easy to install, and energy-efficient.  

Excess ozone in the water breaks down into oxygen which oxygenates the nutrient solution. It helps for fast and healthy root development. Ozone generators are beneficial for odor control in your growing room.  

Air fresheners

You prefer non-aerosol air fresheners to eliminate bad smells in your hydroponics. It can also add a pleasant fragrance to your garden. Meanwhile, we don’t advise you to rely on air fresheners as the primary source of odor control. However, it is handy if you need to mask the unpleasant smell.  

Sterilize the system 

If a pH level problem causes a foul odor in your hydroponic system, you can sterilize your system with water and bleach solution. However, the bleach should not contain chlorine.  

Flush the hydroponic system and replace your nutrient solution more often

One way to reduce the smell is by flushing the system and replacing the nutrient solution regularly. We advise you to replace your solution weekly or about every two weeks. You can set the system up, so the water pipe can be opened easily to drain the system. Make sure to empty your system if there is a low reservoir.  

Drain the nutrient solution into the watering can until the pump begins to draw air. You can add a gallon of pH-adjusted water to the system and run it for about five minutes to flush. Then, you can drain the system again and fill it with a pH-adjusted nutrient solution as well as beneficial microbes.  

Check humidity and heat

It is advisable to check humidity and heat in your hydroponic system. Too much heat can kill your plants and lead to mold growth that can bring unwanted smells.  

Make sure that the nutrient solution is well oxygenated

You can solve your bad odor problem in your hydroponic system if you keep the nutrient solution well oxygenated. It is beneficial to swing the equilibrium in favor of beneficial microbes. It can also offer the plant roots an oxygenated solution. Using an air pump with an air stone to add oxygen to your nutrient solution is good. Remove the stressed or sick plants and plant healthy seedlings only in your system.  

Use only additives and nutrients that are designed for hydroponics

If you want to avoid unpleasant odor in your hydroponic system, make sure to use nutrients and additives that are specifically designed for hydroponic gardening. Don’t use organic fertilizers that are used for soil-based systems. Thus, these can boost the growth of microbes and can have unpleasant results.  

With these solutions, you have assurance that you can have an odor-free hydroponic system.  

Cleaning your hydroponic system 

A dirty and poorly sanitized hydroponic system can lead to foul odor. With this, you should keep your hydroponic garden clean and well-sanitized. Sterilization and sanitation are vital factors for the overall health of your hydroponic plants. It is also beneficial for your health.  

We will reveal some tips on how to clean your hydroponic garden. You should note that each system is different, but here are some general steps you can follow.  

  • Clean everything in your hydroponic garden. You can clean the pipes, reservoirs, pumps as well as nutrient water.  
  • Use clay pellets and other safe nutrients for your plants.
  • Remove dead stems and leaves from your plants to maintain the cleanliness of the nearby area.

Hydroponic system areas to clean 

We recommend you clean your hydroponic system efficiently to make the best of your gardening experience. The following are some areas of the hydroponic system that need to be cleaned.

Anywhere where plants grow in your growing room. Using a similar growing medium can maintain the pH levels and nutrients if the plants return.

Clean air filters monthly to remove bugs and dust.

Wipe down walls in your system 

You can wipe down the lights in your hydroponic system using a damp cloth. We recommend you use alcohol in cleaning the bulbs instead of glass cleaner.

Materials you need for cleaning your hydroponic system. 

Like what we mentioned above, cleaning is an effective way to avoid foul odor in your hydroponic garden. If you want the best cleaning process for your system, you may need the following cleaning materials:

  • Clean rags
  • Bucket and mop
  • Brushes- long-handled and stiff scrubbing
  • Goggles and rubber gloves
  • Clippers to remove dead plants
  • Hydrogen peroxide
  • Compressed air cans for a ventilation system
  • Unscented bleach
  • Garden hose with female hose adapter
  • Alcohol or vinegar for sanitizing

In the cleaning process of your hydroponic system, remember not to clean and mix chemicals without wearing rubber gloves to prevent damage and exposure to yourself. Don’t use heavily concentrated materials for plants. Avoid using too much alcohol and vinegar while cleaning since it can kill the plants.  

Sterilizing and sanitizing your hydroponic system 

Cleaning your hydroponic system is essential for the overall success of your gardening. You can sterilize and sanitize your hydroponics to reduce the smell of your system. Do you want to know the difference between sterilizing and sanitizing?  


Sterilizing happens after harvesting the plants. It is a more intensive process since you will fully clean the physical system to eliminate fungi, viruses, and bacteria. In this stage, you will separate the plants from the system.  


It is a process that is needed by your hydroponic system every two weeks. It helps to get rid of old nutrient water, cleaning the air filters, removing dead plant matter and other grounds for microbes and bacteria that can cause unpleasant smells in your garden.  

Although stopping the unpleasant smell is challenging, note that water can affect your entire hydroponic system. So, as much as possible, keep the water pure.  

Why is it important to eliminate bad odor in hydroponic system?

Naturally, you don’t want an unpleasant smell in your hydroponic system. It can be a nuisance and may bring inconvenience for you and your family. Thus, the foul smell may spread to other areas of your home. The unpleasant odor can be harmful not just to the entire hydroponic system but also to your health.

With that, you should be responsible for removing the unwanted smell from your hydroponic garden. So, you can enjoy safe, healthier, and hassle-free hydroponic gardening. Bacteria buildup that causes a bad smell can also affect your plants, so as much as possible, use growing elements that reduce the growth of bacteria and microbes.  


To sum it up, foul odor is the most common problem you can experience in hydroponic gardening. With the help of this article, we hope that you already know what causes the bad smell and the solutions to stop it.  

Successful hydroponic gardening is possible without suffering from an unpleasant smell. By inspecting your system for possible grounds of odor, you can eliminate them and grow more plants without being overwhelmed by the bad smell.  

Generally, you should be responsible for the maintenance and cleanliness of your hydroponic system. With that, you can avoid the growth of bacteria, microbes, and other elements that can lead to a bad odor.  

You can apply the tips we mentioned earlier to eliminate the foul smell in your growing room. So, you can have a hassle-free and odorless hydroponic gardening. With it, you can grow your favorite plants without suffering from unwanted odor. Do you have a bad smell in your hydroponic system? What are you waiting for? Act and apply the solutions you learned in this article.