Why Is My Well Water Filter Turning Black?

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Using a whole house filter is recommended when getting your water from a well. Even if you have a relatively low level of contamination now, you can’t guarantee that things won’t deteriorate in the future. When you’ve been using a single well for a while, you might notice the amount of contamination increasing over time.

One problem that might eventually develop is your well water filter turning black. This is something that should be addressed as fast as possible, especially if it started happening suddenly and without gradual increase. It could indicate an underlying problem with your water supply.

But why is your well water filter turning black in the first place?

Key Takeaways

Here’s a list of possible reasons why your well water filter is turning black:

  • It may be a problem with the well itself. Consider investigation.
  • Your well water may contain a lot of iron or manganese.
  • Your pipes might be rusty. 
  • Your water may have black sand, silt, or clay in high quantities.
  • Soil or mud entering your water system is also a common reason to get blackened filters.
  • The presence of human/animal waste or other organic matter in your water can also cause a blackened well filter. Check your septic system!
  • Granular carbon may leach from another filter stage.
  • Mold or mildew.
  • Or maybe the filter is simply old and just needs to be replaced.

What Causes Black Sediment in a Well Water Filter?

Black sediment in a well water filter can be caused by a number of factors. It’s difficult to make an estimate about your specific situation without knowing all your individual details – but here are some suggestions for things you should inspect.

A Problem with Your Well

You should start your investigation at the well itself. It’s possible that you might have some problem directly at the source. Depending on the exact cause of the issue, you might need to take immediate action, or simply wait it out.

brown whole house water filter

New Well

It’s normal to see black sediment for the first few weeks after your well has been freshly drilled. The process disturbs minerals, sediment, and other stuff in the soil, causing them to enter your water supply. If your well was installed recently, you may just need to wait a few weeks and the problem will subside on its own.

Improperly Constructed Well

It’s also possible that your well was not installed correctly. For example, it may have been drilled into the wrong location, or based on insufficient ground analysis.

In some cases it’s not about the exact location of the well, but rather its internal structure. If the well was not built properly, it could be allowing contaminants to seep in from the soil.

Collapsed Well

If your well has been installed for a while, it may have recently collapsed. This doesn’t necessarily happen due to improper construction, but could be caused by factors beyond your control. The problem may not always be directly visible through a simple inspection, so it’s best to get in touch with a professional who can investigate the situation.

Well Pump Issues

Your well pump may be malfunctioning or may have been installed incorrectly, causing it to suck up black sediment and contaminants. Keep in mind that this can happen with pumps that have already been operating for a long time. Thus, even if you’ve been using your pump for a couple of years without any issues, you shouldn’t discard that as a possibility.

Damaged Well Screen

A well screen can get damaged over time. And this can sometimes happen when it’s been installed incorrectly, but could also be caused by external factors that could not have been predicted.

In any case, the consequences of a damaged well screen are often similar to what you’d see from an improperly installed or collapsed well.


If your well water contains a high concentration of iron or manganese, it could stain your well water filter black. You normally won’t see any discoloration in the water at its source, but it will develop a characteristic tint once it’s exposed to oxygen.

Rusty Pipes

Black stains could also be an indication of rust originating from your pipes. The issue may not be located directly at the source. It could occur at any point in your plumbing before water reaches the filter.

This issue can be difficult to resolve without redoing your entire plumbing. Usually, one rusted piping segment indicates that you’ll soon see similar problems in other parts of the plumbing.


Sand and similar materials can also cause a black discoloration of your well filter. Usually, they have to be present in very high quantities for this to happen. The location where your well is installed can be a hint that this is what you’re dealing with.


Soil and mud are another common reason to see black stains. If that’s the root cause, it’s usually not a cause for concern as long as your filter is designed to handle contaminants of this type without getting clogged. You might have to replace the filter cartridge more often, though.

Human or Animal Waste

Human and/or animal waste can occasionally make its way into your well water. If you live on a farm or use an external lavatory located close to your well, that’s a high probability.

You might have to rearrange the layout of your property to prevent this from happening in the future.

Other Organic Matter

Organic matter of all kinds can cause black staining and similar issues with a water filter. Depending on the source of the contamination, it may be difficult to remove it completely from your water supply. Advanced filtration may be necessary to address this type of situation.


If you’re using a multi-stage well water filtration system, you might have granular activated carbon (GAC) leaking into the water supply. Check all filters along the chain to ensure that nothing is damaged.

Other Causes for a Black Well Water Filter

The issues we listed above are the most common causes for a well water filter turning black. If you’re not able to tie the problem to any of those factors, here are some additional suggestions to consider.


Mold is a common cause of black discoloration in wet environments. It takes a while to develop, but once it’s started to spread, it can be an alarming issue. It can cause problems with your water filter and spread further into your household, requiring immediate action.

Old Filter

Perhaps it’s simply time to change the well water filter.

You have to be diligent about maintaining water filtration systems and follow the manufacturer’s guidelines about how often the filters should be exchanged. If you forget to do that, the old filter could get clogged up and turn a darker color.

How to Resolve the Issue? Start with Testing!

Some of the above issues boil down to a lack of proper filtration, which can be addressed by testing your water supply and installing appropriate filters. You may be using the wrong type of filter for your situation without even knowing if you haven’t performed any well water testing recently.

Well with Well Cap

Installing Additional Filtration

If you’re dealing with contaminants that your current filtration system isn’t designed to handle, you’ll need to install additional filtration methods. You may be able to expand on your current filter, or you may need to install a whole new unit, depending on the type of filter you’re using and the level of contamination you need to address.

Sediment Filter

A sediment filter is designed to filter sediments by physically blocking them. It doesn’t filter anything else though, so it’s best used in combination with other filter types that attack bacteria etc. which a sediment filter can’t deal with.

Sand Separator

A sand separator specifically targets coarse sand. It usually works through centrifugal force, spinning water fast enough to physically separate the sand particles from the water.

If you live in an area where sand is prone to getting into your water supply, a sand separator is an indispensable step in your overall water filtration.

Manganese/Iron Filter

When dealing with water that’s heavy on iron or manganese, you should use a dedicated filter to deal with those elements. Regular water filters are often insufficient for this, especially when large quantities are involved.

However, make sure to test your water beforehand to avoid wasting money on a filter that you don’t actually need.

Well Inspection

Get a professional to examine your well and look for potential problems within it as soon as possible. Even if you’ve identified a possible cause of your problems, it can never hurt to get an additional opinion and put your mind at ease about the integrity of your well.

You might not have a problem on your hands right now, but there could be one developing beneath the surface – in which case it’s good to get an advance warning that things are about to deteriorate.

Septic System Inspection

Your septic system should be inspected regularly as well. Not just when you’re dealing with problems potentially caused by flaws in it, but in general. Preventative maintenance is a good approach when dealing with something that could so easily introduce health hazards into your drinking water supply.

Replacing Rusty Pipes

Replacing old pipes is usually tricky when they’re underground. But if your well was installed with future maintenance in mind, most of its plumbing should be in an easily accessible spot.

In any case, this requires professional assistance and is not the type of project you’d want to take a DIY approach on.

How Often to Replace or Wash a Well Water Filter?

A well water filter should be replaced regularly to prevent it from accumulating too many contaminants and eventually getting clogged (or turning black). Each manufacturer has its own guidelines about the ideal frequency for replacing filter cartridges.

Sometimes you just need to wash the filter instead of replacing it entirely. Make sure to follow your manufacturer’s instructions as closely as possible to avoid any unpleasant surprises.

If you have any questions about well water filters that turn black please don’t hesitate to leave a comment below!

About the Author Gene Fitzgerald

Gene Fitzgerald is one of the founders of BOS and currently head of content creation. She has 8+ years of experience as a water treatment specialist under her belt making her our senior scientist. Outside of BOS, Gene loves reading books on philosophy & social issues, making music, and hiking.
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