What to Do About Algae in a Whole House Water Filter

🤝 Our content is written by humans, not AI robots. Learn More

Your whole house water filter system is supposed to protect you from nasties in your water – so it can be a bit of a shock to discover slimy, green algae growing inside your filters.

In this guide, we’ll be sharing all the most important information about algae in a whole house water filter, including how it gets there, its potential health effects, how to remove it, and more.

📌 Key Takeaways:

  • There are several reasons why algae might grow in a whole house water filter system, including if the system is located in a warm, moist place, or due to a lack of disinfectants in the water.
  • Algae can be found anywhere, and needs only sunlight and water to grow.
  • Water is likely to contain algae if it’s exposed to light, warmth, and certain nutrients, like nitrates and phosphate.
  • Well water is more susceptible to algae than chlorinated city water.
  • You can remove algae from water by shocking your well or using a pump to purge your well.

🧫 Why Does Algae Grow On A Whole House Water Filter?

If you’re wondering, “why is my whole house water filter green?” we’re here to answer this question.

Green filters are most likely caused by algae, a type of photosynthesizing organism that grows in water or on surfaces that come in contact with water.

Algae might grow on a whole home water filter system for the following reasons:

  • The water filtration process greatly reduces disinfectants like chlorine and chloramines, which are used to keep algae at bay
  • Filtered water has minimal turbidity, which is ideal for algae growth
  • Your filter might be located in a warm, humid location, or a location that gets direct sunlight
  • Your water might be sourced from a location that’s prone to blue-green algae formation, like a lake or a private well
Algae growth in water filter cartridges

Where Does Algae Come From?

Algae doesn’t technically “come from” anywhere. It only needs water and sunlight to grow, so don’t be too surprised if you discover it in your water filter, even if your water source doesn’t contain algae spores.

Even simply installing your water filter unit close to a window will increase the likelihood of algae buildup in the system.

With that said, algae is more likely to grow in water sources that already contain algae.

🩺 Potential Health Risks of Algae

There are hundreds of types of algae found today, and some are more harmful than others. It all depends on the types of toxins produced by the algae.

For instance, blue-green algae bacteria is considered one of the most toxic forms of algae, and is known to cause respiratory issues, vomiting, headaches, diarrhea, and hay fever-like symptoms when ingested.

If you’re not sure whether or not your water contains blue-green algae or another form of algae, get it tested. Professional testing data will tell you exactly what you’re dealing with, so you can take the appropriate action to resolve the problem.

Water testing with tap score

🚰 How to Clean Algae From a Whole House Water Filter: 6 Steps

You can clean algae from a whole house filter by following these 6 simple steps.

You will need:

  • Light dishwashing detergent
  • A soft sponge


  1. Disassemble the system by removing the cartridges from the filter housing. Put the cartridges to the side.
  2. Wash the filter housings in warm water with dishwashing detergent. Use a soft sponge to wipe algae off the surfaces. Make sure to get into the cracks and crevices.
  3. Rinse the filter housings thoroughly.
  4. Leave the filter housings to dry and rinse the water filters under running water.
  5. If the water filters are badly affected by algal blooms, replace them with a new set of filters.
  6. Allow everything to air-dry, then reassemble the system.
Whole house water filter cartridges

🚫 How to Prevent Algae From Growing on a Whole House Water Filter

Let’s be honest – you’d rather not get green algae on your water filter in the first place. How can you prevent potentially toxic algae from growing in your whole home filter and save yourself the regular cleaning job?

There are a few ways to prevent algae buildup:

  • Install your system in a cool, dark location, away from warm temperatures and humidity (algae grows quickest at 68 °F-86 °F)
  • Build a box around your unit to prevent sunlight from getting into the filters
  • Clean your water tank at least twice a year
  • Install a filter sleeve for UV protection if available

🤔 Why Does Water Contain Algae?

What if your drinking water contains algae, and that’s what’s causing algae to grow in your whole home filter?

There are a few reasons why tap water might contain algae.

Well water is much more likely to contain algae than city drinking water.


Because well water typically has a much higher concentration of nitrogen and phosphorus – two nutrients that promote the growth of algae.

Plus, wells have minimal movement or turbulence, providing the stability algae needs to grow. Wells are also more likely to be in a location that receives direct sunlight, which is essential for algae formation.

Even if your water doesn’t come from a private well, it’s at risk of containing algae if it has a high pH or low turbidity.

Usually, algae grows due to a combination of the conditions mentioned above.

Algae growth in water

❌ How to Prevent Algae From Contaminating Water

Algae looks gross, and you don’t want to drink something that might produce harmful toxins. Luckily, you can prevent algae from contaminating your water and clogging your filtration system.

There are two ways to achieve this:

Purge Your Well

If you have a major algae issue inside your well, your only solution might be to purge your well. You can use a pump to do this. For best results, you’ll need to purge a minimum of three well volumes of water.

Shock Your Well

If you don’t fancy pumping that amount of water, consider shock-chlorinating your well.

We shared an in-depth guide on how to shock-chlorinate a well here. If you just want a quick overview, here’s what to do:

  1. Add chlorine bleach to your well. The exact amount you need depends on the size (depth and diameter) of your well. If you’re unsure, check out the CDC guidelines.
  2. Run clean water into the well using a clean hose.
  3. Continue to rinse the well casing for a minimum of 10 minutes. This will get rid of chlorine traces.
  4. Turn on all the faucets in your home and run them until you can no longer smell chlorine in the water.
  5. Switch off the faucets. Leave your well (and don’t drink the water) for 12 hours.
  6. Drain your well to remove the chlorinated water.
  7. Turn on all the faucets in your home and repeat the earlier process. Run the faucets until no more chlorine can be detected.
  8. For the first 48 hours after shock-chlorinating your well, boil your water to evaporate the chlorine before drinking it.

Related Article: Everything to know about showering after chlorinating a well

📝 In Summary

Algae in a whole home filter system can be concerning, but thankfully, it’s easy to deal with – and can be prevented in the future.

You can use dishwashing soap and warm water to clean algae off filter housings, and rinse filter cartridges to remove algae inside the media. You might need to replace the filters in severe cases of algae accumulation.

Ultimately, you can prevent algae from growing in your water filter by ensuring the filter is located away from heat or direct sunlight, and by installing a UV purifier to eliminate algae from your water supply. You can prevent algae from forming in the first place by shock-chlorinating or pumping your well.

  • Jennifer Byrd
    Water Treatment Specialist

    For 20+ years, Jennifer has championed clean water. From navigating operations to leading sales, she's tackled diverse industry challenges. Now, at Redbird Water, she crafts personalized solutions for homes, businesses, and factories. A past Chamber President and industry advocate, Jennifer leverages her expertise in cutting-edge filtration and custom design to transform water concerns into crystal-clear solutions.

2 thoughts on “What to Do About Algae in a Whole House Water Filter”

  1. Avatar for Jennifer Byrd

    Hi Jennifer. Excellent article. I learned a lot. My rural house has a cistern which is regularly filled by a water delivery service which uses a municipal water supply. Our system is bothered by a golden algae which clogs the screen filers in appliances such as toilets and washing machine. I have to clear the toilet screens every two weeks. We treat each water delivery with a cup of bleach, but it does not make a difference. Do you have any suggestions to remedy this? Should we try adding more bleach? Is there an algaecide suitable for drinking water use? Thanks so much.

Leave a Comment

Your email address will not be published. Required fields are marked *

Scroll to Top