Clogged Well Water Filter – Learn How to Fix NOW

Author: Jason Hollow - Published: 2022/10/20 - Updated: 2022/12/22

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Well water filters are prone to clogging since they often deal with larger amounts of sediment and other contaminants. If your filter experiences a clog, you should deal with it as soon as possible.

If you are unsure of the causes responsible for a clogged well water filter and what to do about it, read on to find out.

So, here is our step-by-step guide on how to unclog your well water filter the right way!


These are the most common causes for a clogged well water filter and how to fix them:

  • Sediment – You can wash or backwash the filter
  • Organic matter – You can use a chemical cleaning agent to eliminate it from your system
  • Limescale – You can use descaling solutions that can effectively dissolve scale deposits like calcium and magnesium
  • Rust – There are many rust removal products in the market
  • Worn-out filter – Replace filter cartridge, which also solves all of the problems above

What Causes Well Water Filters to Clog?

There are a number of reasons why well water filters get clogged, including sediment in the water and high iron levels:

Sediment Build Up

Sediment in well water can be caused by sand, silt, or other particles mobilized by storms, erosion, or the decomposition of organic matter. It’s pretty normal to find some sediment in well water, but an excessive buildup of this material can end up clogging your water filter.

Older water wells, in particular, are more susceptible to sediment problems as the sediment builds up over time. On top of clogging issues, this can also cause damage to the well pump.

Algae and Bacteria

Since well water is drawn from natural water sources, it’s a perfect breeding ground for bacteria, algae[1], and other microorganisms.

Not all forms of bacteria are harmful. However, some, like coliform bacteria, can cause diseases and other health problems. Algae, on the other hand, isn’t necessarily dangerous but will alter the appearance of your water.

A buildup of algae or bacteria can also cause your well’s filter to clog up.

Hard Water

Hard water, or water with higher mineral content, can cause limescale build up inside your pipes and mess with your plumbing. While these minerals aren’t a problem for your health, it will be an issue for your filter.

Problems Caused by a Clogged Well Water Filter

clogged well water filter thumbnail

When you have a clogged well water filter, you’ll notice that the water won’t flow as effectively. However, that’s only one of the issues that come with a clogged filter.

A clogged well filter system can end up damaging your water pump due to the additional strain necessary to work, causing the pump to overheat or even break down.

Additionally, if your filter is clogged, the water won’t be processed thoroughly, which could lead to harmful contaminants leaking into your home’s water supply, causing a myriad of health problems such as skin infections, gastrointestinal illness, and others.

How to Unclog a Well Water Filter

Before you can start the process of unclogging a well water filter, you need to know what caused it to clog up in the first place. Understanding the cause of the clog will then let you know the steps you need to follow in order to fix the problem.

Here are some examples of how to fix a clogged well water filter, depending on the cause of the clog:

  1. Filter clogged with sediment: Sand, silt, and other forms of sediment can be cleared from your filter by washing it. Simply run water in the opposite direction to flush out the sediment particles.
  2. Filter clogged with organic matter: For algae, bacteria, or other organic matter, you can use a chemical cleaner. Whenever you work with chemicals, make sure to wear gloves and follow the instructions to the letter.
  3. Filter clogged with minerals (hard water): A descaling solution will help you clear a well water filter clogged with calcium, magnesium, or other similar minerals. Mineral deposits will be dissolved by the solution, making it easier to remove them.
  4. Filter clogged with rust: Use a rust removal product on filters clogged with rust. You can acquire these products at most hardware stores, and you just have to follow the instructions in the package.
  5. Old well water filter: The source of the problem might not be an external factor. It could be that your well water filter has reached the end of its usable life. If your well water filter is too old, simply replace it. Depending on your type of filter, this may be a simple process, or you may require professional assistance.

How Often Should Your Filter Be Replaced?

The frequency with which you’ll have to replace your well water filter will depend on a wide variety of factors, including its model, the quality of your water supply, and how much water you use in your home.

Each manufacturer gives you a range of time for the filter replacement based on the water usage of a “standard” household.

Smaller filters and those that are used more frequently, such as a point-of-use drinking water filter, will need more frequent replacement. On the other hand, a whole house unit, such as a carbon media filter, will last you up to a few years in between replacements.

In general, you’ll want to check your system’s condition every few months and replace/clean a filter when it clogs up.

Well Water Filter Types: Which One Is Best for You?

There are many different types of well water filters available, but choosing the right one for your home will largely depend on your specific water filtration needs.

In order to know what you are dealing with, you’ll need to have your water tested.

As for the types of well water filters available, here’s what you can choose from:

Whole House Water Filters

Whole house water filters work their magic right at the water’s point of entry to your home. Since they operate directly at the source of entry, they filter all the incoming water meaning all taps, showers, and faucets will have clean water.

If you are looking for a system that protects not only your family but also your plumbing and appliances, this is the way to go.

Whole house water filters usually have multiple stages of filtration, each dealing with a specific type of contaminant. Pre-filters usually handle sediment, or larger physical particles, while the main filter might take care of pesticides and other chemicals.

A post-filtering stage may be used to improve water taste and odor.

Point-of-Use Water Filters

Point-of-use filters are installed directly on a tap or faucet and as such, only provide clean water for that specific water outlet. POU filters are easy to install, use, and are generally more cost-effective than other options, though often they are not as thorough when it comes to their filtration capabilities.

You can also combine whole house and POU water filters for additional protection.

Reverse Osmosis Systems

under sink reverse osmosis system with storage tank

Reverse osmosis systems filter water by forcing it through a semipermeable membrane, removing a wide range of contaminants in the process. They can either be POU or whole house systems, depending on the installation location.

UV Water Purifiers

Ultraviolet water purifiers use UV light to kill organic contaminants, such as viruses, bacteria, and algae, making them an excellent choice for dealing with pathogens in your water.

However, their effectiveness can be significantly compromised by physical particles in the water. If your water has a high hardness or turbidity level, you might be better off with another system.

Why Do You Need a Filter for Well Water?

Since well water comes from untreated natural sources, it is most likely to contain some form of contamination.

However, in some cases, well water is safe enough to drink without requiring any filtering. Testing your water is the only way to determine if it needs filtering.

Getting Your Well Water Tested

It’s important to test your well water in order to understand what kind of contaminants you are dealing with, as this is the only way that you can effectively deal with clogging issues or other filtration problems.

If you need your water tested, get in touch with your local health department or environmental organization so they can let you know how to proceed.

You can also test the water on your own by means of a DIY water testing kit, but the results won’t be as accurate or thorough as if you had it tested at a lab.


The process of unclogging your well filter will depend on what caused the obstruction.

There are multiple causes for a clogged well filter, including sediment build-up, algae, and water with high mineral content (hard water).

Sediment clogging can be dealt with by washing the filter, while algae build-up will require a chemical cleaner.

If your well filter clogs frequently, consider installing an additional pre-filtration that specifically targets the cause of the clogging.

Further Reading


Meet Jason Hollow

Jason Hollow Jason is the founder of Water Masterz and head of content creation. After six years in the industry, he has tremendous knowledge and first-hand experience on all things related to water treatment.

His credo: Not a single American should have to drink unhealthy water at home.

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