How to Dechlorinate Water for Aquaponics: Safe Top-Ups and Water Changes
How to Dechlorinate Water for Aquaponics Safely
Tap water might look clean and safe, but that doesn’t always mean it is ready to go straight into your aquaponics system.
Most town water is treated with chlorine or chloramine to control harmful microbes. That is helpful for our drinking water, but not so helpful for the fish and beneficial bacteria keeping an aquaponics system alive.
Whether you are filling a new system, replacing water or simply topping up what has evaporated, preparing the water first is one of those small jobs that can prevent a much bigger problem later.
Here’s how to dechlorinate water for aquaponics safely and protect the balance you have worked so hard to create.
Why Dechlorination Matters (and What Happens If You Skip It)
Tap water is often treated with chlorine or chloramine to kill harmful microbes. But those same chemicals will also kill or damage your nitrifying bacteria and stress or injure your fish if introduced into your aquaponics system.
Chlorine rapidly kills bacteria and can cause gill, mucus or respiratory stress in fish.
Chloramine is a compound formed using chlorine and ammonia. It is more stable and harder to remove. When chloramine is neutralised, ammonia may remain in the water depending on the product used. In a mature system, established nitrifying bacteria may process a small amount, but it is still important to use the correct dose and monitor ammonia after a substantial top-up or water change.
When water with chlorine or chloramine touches your biofilter and beneficial bacteria, it can wipe out the colonies you’ve carefully established. That’s exactly what you don’t want.
That’s why every time you add or top up water, you must ensure it’s safe, either aged, treated or dechlorinated.
What Is Aged Water, and Is It Safe for Aquaponics?
Aged water means letting tap water sit for a period, usually 24–48 hours, so that free chlorine can evaporate naturally. But:
It doesn’t reliably remove chloramine because chloramine won’t evaporate as easily as chlorine.
If you pour untreated water straight over your biofilter media, you risk subjecting the bacteria to residual disinfectants.
A better practice is to keep a separate drum or container of dechlorinated or aged water dedicated to topping up. Let the water stabilise before adding it to your system. Free chlorine may dissipate when water is left standing and aerated, but the time required varies. Chloramine does not reliably disappear through ageing or aeration and should be removed with a treatment specifically designed for chloramine.
Topping Up (Evaporation Compensation): How to Do It Safely
Because aquaponics systems lose water to evaporation, you’ll often need to top up. Here’s a safe protocol:
Keep a reserve tank or drum filled with tap water that’s been dechlorinated or aged.
Aerate the reserve water using an airstone or pump. This helps dissipate dissolved gases and promotes gas exchange.
Match temperatures before adding. Avoid sudden shocks by matching the reserve’s temperature to your system’s water.
Add slowly and carefully, ideally to the sump or surge tank, not directly to grow beds or over biofilter media.
It’s much easier to prepare your top-up water properly than to repair a stressed system afterwards. That little bit of planning helps protect your fish, your bacteria and the balance you’ve worked so hard to build.
Learn how to build a simple solids waste filter for your aquaponics system:
Methods for Dechlorinating Water
Let’s compare the options: aeration and passive methods, chemical dechlorinators and vitamin C methods, with their pros, cons and caveats.
1. Aeration and Passive Methods (Letting It Sit and Airing)
Letting water sit for 24–48 hours may allow free chlorine to dissipate.
Aeration helps by increasing gas exchange and gently driving off residual chlorine.
Limitations: It doesn’t reliably remove chloramine, which is more stable.
Best used when your tap water only has free chlorine and no chloramine.
2. Chemical Dechlorinators (Commercial Conditioners)
These typically use sodium thiosulfate or similar compounds that neutralise chlorine and chloramine quickly.
Pros: Fast, effective and safe when used correctly.
Cons: Some products only deal with chlorine and not chloramine, unless they are formulated for both.
Choose a conditioner labelled for both chlorine and chloramine, and follow the dosage instructions carefully. Adding more than the recommended amount does not necessarily make the water safer and may affect water chemistry depending on the product.
Aquarium dechlorinators may contain treatments for both chlorine and chloramine and can be safe to use with fish when the manufacturer’s instructions are followed. Treating the water in a separate drum makes it easier to confirm the dose, aerate the water and allow its temperature to move closer to the aquaponics system before it is added.
3. Vitamin C (Ascorbic Acid or Sodium Ascorbate)
Some research and technical reports show that vitamin C can effectively neutralise chlorine.
In a US Forest Service technical report, both ascorbic acid and sodium ascorbate neutralised chlorine rapidly. However, ascorbic acid can lower the pH of treated water when used in large doses, while sodium ascorbate is pH-neutral and is less likely to affect the water’s pH.
The report focuses on treating chlorinated water rather than its use in an aquaponics system. It also does not provide a complete aquaponics-specific method for treating chloramine.
Vitamin C, therefore, shows promise for removing chlorine, but the correct dose needs to be calculated carefully. For most home aquaponics systems, a fish-safe conditioner labelled for both chlorine and chloramine may be the simpler option.
If using vitamin C, test the treated water before adding it to your aquaponics system and monitor the pH, particularly when using ascorbic acid.
Learn more about how pH can impact your aquaponics setup:
Impacts on Fish and Bacteria from Chlorine and Chloramine
Even small amounts of chlorine will kill or damage nitrifying bacteria, disrupting your biofilter function.
Fish exposed to chlorine or chloramine may suffer gill damage, respiratory stress or death in severe cases.
When chloramine is neutralised, ammonia may remain in the water, depending on the treatment used. This can be especially dangerous in a new system without enough established bacteria to process it.
Thus, introducing non-dechlorinated water is one of the fastest ways to destroy your system’s balance.
Putting It All Together: Safe Water Handling in Aquaponics
Always dechlorinate new water before adding it to your system.
Use a separate drum with aeration as your top-up water reserve.
Avoid directly pouring tap water over biofilter media or grow beds.
Test your water regularly for chlorine, pH and ammonia, especially after topping up.
Always check whether your local water supplier uses chlorine or chloramine, as treatment practices can change.
Buffering and filtration help maintain stability so that any slight residuals or pH shifts don’t stress your system.
When handled carefully, your water additions support rather than harm your balanced, self-sustaining aquaponics ecosystem.
Frequently Asked Questions
Can I Put Tap Water Straight Into an Aquaponics System?
Tap water should not be added directly unless you have confirmed that it contains no harmful chlorine or chloramine. Treat and test the water before adding it to protect your fish and beneficial bacteria.
How Long Should Tap Water Sit Before Adding It?
Water containing free chlorine is often left for 24–48 hours with aeration, although the time required can vary. Leaving water to stand does not reliably remove chloramine.
Does Aeration Remove Chloramine?
No. Aeration may help free chlorine dissipate, but chloramine is more stable and should be removed with a treatment specifically labelled for chloramine.
Can I Use Aquarium Water Conditioner in Aquaponics?
A fish-safe aquarium conditioner can be suitable if it is labelled for both chlorine and chloramine and is used according to the manufacturer’s instructions.
Where Should I Add New Water to My System?
Add treated water slowly, ideally into the sump or surge tank, rather than pouring it directly over the grow beds or biofilter media.
Protect Your Aquaponics System With Safer Water
Preparing your top-up water may feel like one more job, but it is much easier than trying to restore a system after chlorine or chloramine has affected your fish and beneficial bacteria.
Use a separate reserve drum, choose a treatment suited to your local tap water and test when needed. These simple habits help protect the living balance that keeps your aquaponics system healthy.
Learn More About Aquaponics
Check out the COURSES page to learn how you can get started with aquaponics now. Click HERE.
Want to get your Eyes and Hands on the FREE Online Aquaponics Essentials Course?
This is a great free resource to really understand how aquaponics is a sustainable ecosystem that will grow your organic food is a productive way.
You learn how all the 'parts' make up the 'whole', and helps to give you the foundations of understanding aquaponics.
Sign up HERE
Check out my YouTube Channel 'Candy The Aquaponics Lady'
Aquaponics is an ecosystem, and with anything it takes time to learn how it works. So, sit back and binge watch my 'how to' playlist and the 'Water Quality Made Simple' Playlist, and learn the next steps in your aquaponics system as you create the ecosystem.
Here are the next 2 videos I recommend you watching to create your ecosystem ~ before you add any fish
How Aquaponics Works as an Ecosystem
Why aquaponics is the best form of gardening for you
Learn More About Aquaponics
Check out the COURSES page to learn how you can get started with aquaponics now. Click HERE.
Want to get your Eyes and Hands on the FREE Online Aquaponics Essentials Course?
This is a great free resource to really understand how aquaponics is a sustainable ecosystem that will grow your organic food is a productive way.
You learn how all the 'parts' make up the 'whole', and helps to give you the foundations of understanding aquaponics.
Sign up HERE
Want to help out (donate some fish food) and Feed my Fish?? (They don't drink coffee)
Candy Alexander is a dedicated aquaponics enthusiast with a wealth of formal training in aquaculture. Over the past 15 years, Candy has been deeply immersed in both commercial and backyard aquaponics, honing her skills and expertise in this sustainable farming method.
Candy's passion lies in making aquaponics accessible to everyone. With a mission to simplify aquaponics, she believes that anyone can embark on this sustainable journey.
She encourages those new to aquaponics to "kick the tires" without a significant financial investment. Her guidance focuses on helping people start their aquaponics journey with small-scale systems, ensuring a low barrier to entry for newcomers.
Candy shares practical tips, step-by-step guides, and personal stories to inspire and guide readers on their aquaponics adventure. Whether you're a seasoned farmer or a curious beginner, Candy Alexander is your go-to source for simplifying aquaponics and fostering a sustainable gardening experience.
