How to Dechlorinate Water for Aquaponics

Water is the lifeblood of an aquaponics system. It is where fish and plants coexist in a delicate balance. While tap water is readily available for many of us, it often contains chlorine, which is not good for aquaponics systems. The chlorine, which is added to the tap water supplies to make it safe for human consumption, can be detrimental to the health of both fish and plants in your aquaponics system.

In this article, we will discuss the process of dechlorinating water for your aquaponics system. Whether you're a seasoned aquaponics enthusiast or just starting out on your aquaponic journey, knowing how to remove chlorine from your water source is crucial to the success of your system. 

Why Chlorine is Added to Tap Water

Chlorine is a common chemical disinfectant added to the tap water supplies. This process helps remove harmful bacteria, viruses, and other microorganisms in the water that could pose serious health risks to people. This is a crucial step in water treatment that plays a significant role in reducing the prevalence of waterborne diseases and ensuring public health.

The addition of chlorine to tap water is often referred to as chlorination. During this process, chlorine gas or chlorine-based compounds are introduced to kill or deactivate harmful microorganisms, making the water potable. While this is essential for human health, it can be problematic for aquaponic systems, where fish and plants can be exposed to the same treated water.

The Potential Harm of Chlorine to Aquaponics Systems

Here are some of the potential harms of using chlorinated water for your aquaponics system.:

  1. Toxicity to Fish: Chlorine is toxic to fish, even in relatively low concentrations. When fish are exposed to chlorinated water, they may exhibit signs of distress, such as gasping at the water's surface, erratic swimming behavior, and increased stress levels. 
  2. Impact on Beneficial Bacteria: Aquaponics systems rely on beneficial bacteria to convert fish waste into plant nutrients through the nitrogen cycle. Chlorine can disrupt this process by harming or killing these essential bacteria, causing ammonia levels to rise and negatively affect water quality.
  3. Plant Growth Inhibition: Chlorine can also hinder plant growth by damaging the delicate root systems of aquaponic plants. 

The potential harm that chlorine can inflict on both fish and plants within an aquaponics system makes effective chlorine removal in the water a necessity. It is essential to remove chlorine from the water before introducing it to your aquaponics setup in order to maintain a thriving and balanced system.

Chlorine Test Strips

The Different Methods of Dechlorinating Water

Below are the three methods of dechlorinating water. Each of these methods offers advantages and disadvantages that allow you to select the one that best suits your needs and preferences. 

1. Chlorine Evaporation

Chlorine evaporation, or letting the water set, is a natural and chemical-free method of dechlorinating water. This methodinvolves allowing tap water to sit in an open container for a period of time. During this time, chlorine will naturally dissipate as it is exposed to air.

To facilitate chlorine evaporation:

  • Simply fill a container, like a bucket or tank, with tap water and let it sit exposed to the air. The surface area and water movement can affect the speed of evaporation.
  • Usually, it takes 24 to 48 hours for chlorine to completely evaporate from tap water. This time frame can be shorter or longer based on factors like temperature, humidity, and initial chlorine concentration.

Advantages and disadvantages of chlorine evaporation:


  • Low-cost and straightforward.
  • Suitable for smaller aquaponics systems.


  • Slow process.
  • Not suitable for quickly dechlorinating large volumes of water.

2.Using Dechlorination Agents

The dechlorination agents are chemicals specifically designed to neutralize chlorine and chloramines (a more stable form of chlorine). The most commonly used dechlorination agents are sodium thiosulfate and sodium bisulfite, which are available in liquid or powder form.

This method is a fast and effective method that provides almost instant results and is suitable for small and large aquaponics systems. However, this method requires a small investment, as you may need to purchase dechlorination agents. It is also important to follow proper dosing guidelines to avoid over- or under-dosing.

Advantages and disadvantages of using dechlorination agents:


  • Fast and effective.
  • Applicable to various system sizes.


  • Requires purchasing dechlorination chemicals.
  • Careful dosing is essential to prevent overdosing or inadequate treatment.

3.Activated Carbon Filtration

Activated carbon filters are often used in aquariums and water purification systems and rely on activated carbon to remove chlorine and impurities from water. Activated carbon is highly porous and has a large surface area, which allows it to absorb chlorine molecules as water passes through the filter. The chlorine molecules adhere to the carbon's surface, effectively removing them from the water.

Advantages and disadvantages of using carbon filtration:


  • Continuous dechlorination.
  • Enhances overall water quality.


  • Initial setup and maintenance costs.
  • You need to regularly replace the activated carbon media.

Our Recommended Dechlorinators for Aquaponics

The tap water you use to fill up your fish tank may contain chlorine or chloramine, which can be harmful to the fish and plants. To remove chlorine, you need to treat your water with a dechlorinator or water conditioner. Here are some of our recommended dechlorinators for aquaponics.

1.Seachem Prime

Seachem Prime Fresh and Saltwater Conditioner

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Seachem Prime Dechlorinator is a must-have for aquaponics enthusiasts. It effectively removes chlorine, detoxifies harmful chemicals, and maintains stable water conditions. The concentrated formula is cost-effective, and it doesn't harm beneficial bacteria. It's an essential tool for keeping your fish and plants healthy in your aquaponics system. Highly recommended!

2.Crystal Clear Vanish Plus Liquid Dechlorinator

CrystalClear Vanish Plus Liquid Dechlorinator

Crystal Clear Vanish Plus Liquid Dechlorinator effectively eliminates chlorine and chloramine from tap water. Its easy-to-use liquid form allows for precise dosing, and a little goes a long way, making it cost-effective. It also helps maintain stable water conditions and doesn't harm the beneficial bacteria, which is crucial for the nitrogen cycle. 

3.Tetra AquaSafe Plus Water Conditioner

Tetra AquaSafe Plus

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This product efficiently removes chlorine and chloramine from tap water, which ensures the safety of fish in the tank. Its easy-to-measure dosing cap makes it a breeze to use, and it's cost-effective because of its concentrated formula. The Tetra AquaSafe Plus Water Conditioner also helps maintain stable water conditions and doesn't interfere with the beneficial bacteria in the system.

4.Home Grown Ponics Instant D-Klor

Instant D-Klor

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The Home Grown Ponics Instant D-Klor excels at swiftly neutralizing chlorine and chloramine in tap water. It's an easy-to-use design makes dosing a breeze, and its cost-effectiveness is a bonus. It also helps maintain stable water conditions without disrupting the beneficial bacteria essential for a healthy system.

5.API TAP Water Conditioner

API TAP Water Conditioner

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API TAP Water Conditioner is a must-have for aquaponics. It quickly and effectively removes chlorine, chloramine, and heavy metals from tap water, ensuring the safety of your fish and plants. Easy to use and gentle on beneficial bacteria, it's a reliable solution for maintaining water quality in your aquaponics system.

Best Practices for Dechlorinating Water

1.Testing for Chlorine Levels

Testing water for residual chlorine levels is a critical step in ensuring the success of your dechlorination process. Regular testing helps you confirm that the water is safe for your aquatic and plant inhabitants.

Recommended test kits and methods for testing chlorine:

Below are several methods and test kits available for measuring residual chlorine levels in water. Choose a testing method that suits your needs and budget, and follow the manufacturer's instructions for accurate results.

  • Chlorine Test Strips: These strips change color in the presence of chlorine, providing a quick and simple visual indication of chlorine levels.
  • Liquid Test Kits: Liquid test kits typically involve adding reagents to a water sample and observing color changes to determine chlorine concentration. They often offer more precise measurements than test strips.
  • Digital Chlorine Testers: These electronic devices provide accurate and digital readouts of chlorine levels and are often preferred for their reliability and ease of use.

2.Monitoring Water Quality

Monitoring water quality in your aquaponics system should be a routine practice. Regular checks ensure that your system remains healthy and balanced. After dechlorinating the water and setting up your aquaponics system, continue to monitor key water parameters like pH, ammonia, nitrite, nitrate, and temperature.

Tips for Dechlorinating Water

Here are some additional tips and best practices to ensure that your dechlorination process is successful:

  1. Test the Water Source: Regularly test the tap water source for chlorine levels. This will help you determine the chlorine concentration and whether it fluctuates, allowing you to adjust your dechlorination methods accordingly.
  2. Use a Dechlorination Agent When in Doubt: If you're unsure about the chlorine levels in your tap water or if you suspect that chloramines may be present, consider using a dechlorination agent like sodium thiosulfate or sodium bisulfite as a precaution.
  3. Monitor Water Quality Continuously: Invest in a water quality monitoring system that can provide real-time data on parameters like chlorine levels, pH, temperature, and ammonia. This allows you to respond promptly to any water quality issues.
  4. Plan Ahead: Dechlorinate water before introducing it into your aquaponics system. This ensures that your fish and plants are not exposed to chlorine or chloramines, reducing stress and potential harm.
  5. Maintain Adequate Water Flow: In systems with active water circulation, ensure that the dechlorinated water has enough time to mix and circulate within the system to evenly distribute the treated water.
  6. Regularly Clean Filters: If you are using activated carbon filtration, ensure that the filter media is clean and functioning optimally. Regular maintenance of your filtration system is essential for effective dechlorination.

Alternative Water Sources


Benefits of using rainwater:

  • Rainwater is naturally soft and free from chlorine, making it an ideal water source for aquaponics.
  • Since it's not treated with chemicals, rainwater eliminates the need for dechlorination, reducing stress on fish and plants.
  • Collecting rainwater aligns with sustainable practices, reducing the demand for municipal water supplies.
  •  Once set up, rainwater collection is a cost-effective solution.

How to properly collect and store rainwater:

  1. To collect rainwater, you'll need a suitable gathering surface like a roof. Ensure the surface is clean and free from contaminants.
  2. Install gutters and downspouts to direct rainwater from the roof into collection tanks.
  3. Use screens or mesh filters to remove debris and large particles from the rainwater as it enters the collection system.
  4. Store rainwater in clean, food-grade storage tanks designed for water storage. 
  5. lean gutters, downspouts, and storage tanks periodically to maintain water quality.
  6. Regularly test rainwater for pH, nutrient levels, and other water quality parameters to ensure it meets the needs of your aquaponic system.

1.Well Water

Benefits of using well water for aquaponics:

  • Well water typically provides a consistent and reliable source of water throughout the year.
  • Well water is often free from chlorine, reducing the need for dechlorination.
  • Some well waters contain beneficial minerals that can enhance plant growth.


The significance of water quality in aquaponics cannot be overstated. This is why ensuring that the water in your system is free from chlorine, a potential threat to the health and vitality of your fish and plants, is important.

Understanding the chlorination process in tap water, the potential harm it poses to aquaponics systems, and the necessity of chlorine removal provides the foundational knowledge needed for success. Whether you choose natural chlorine evaporation, dechlorination agents, or carbon filtration, the key lies in thorough dechlorination before introducing water to your aquaponics ecosystem.

Remember, it does not end with just dechlorinating water. Regular testing and monitoring of the water quality is key in ensuring the overall health and success of your aquaponics system. 

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