What to do When Your Whole House Water Filter Gets Black

Author: Jason Hollow - Published: 2022/09/28 - Updated: 2023/01/05

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You don’t have to panic about a black whole house water filter, but you shouldn’t ignore it either.

Whenever your water changes colors, the safest thing to do is figure out what’s causing the change. A black water filter problem could simply indicate the need to replace it more often, but it is best to know for sure.

This article will explain why your whole house water filter has turned black, what your water supply has to do with it, and how you can resolve the issue.

So, here is our guide on what to do when your whole house water filter turns black!


  • Have your water professionally tested to figure out the cause of why your water is turning black.
  • The most common reasons are due to the presence of iron, manganese, or black sediment.
  • Also inspect your entire whole house water filter setup, especially if a carbon filter is leaking or needs replacement.
  • Look for signs of rust or corrosion in your pipes and water heater.
  • It is not uncommon for the cause to be due to a new or collapsed well.
  • You can have a professional inspect your septic system to see whether it releases contaminants that sip into your source water.

Help, My Whole House Water Filter Turns Black!

black whole house water filter thumbnail

There are numerous reasons why your whole house water filter is turning black. Most have to do with the water source. These reasons include:


A black whole house water filter is typically caused by iron or rust in the water supply. Older plumbing in your home or well water with excessive iron levels can cause rust and iron to accumulate in a water filter.


Another common cause of filters and water turning black is manganese. Manganese, like iron, can be found in well water when it leaks from the ground.[1]


If your water comes from a well, the well’s sediment could cause the water’s color. Black sediment could be caused by one of two things:

  1. Organic matter – You may occasionally find organic particles in your well water, such as algae or bacteria. As a result of these particles, your pipes and whole house water filter could become clogged over time, resulting in dirty/black water.
  2. Sediment – Well water absorbs sand and silt as it passes over rocks and dirt, which accumulates over time and causes your filter to become black or brown. Despite not being particularly harmful for your health, black sand and silt can still reduce water quality.

Mold or Mildew

A lack of ventilation or excessive humidity could cause mold or mildew to grow in your home, which on top of turning your water black, can also cause the water to smell musty. If you notice this smell in your water, get it tested for contaminants as soon as possible.

Carbon Filter Media

In the case of whole house water filters that use activated carbon as their filtering media, the black hue is likely caused by carbon particles escaping from the filtration element.

This should not cause alarm.

Your Septic System

Your house’s water filters might also become blackened due to a failed septic system. Septic tanks can leak sewage into well water, which is filtered by your whole house water filter.

Your Private Well

A New Well

For a period, newly dug wells might cause your water to appear dirty or discolored. The process to construct your well will release a lot of sediment or minerals, which could leak into the water at first. These particles may take some time to clear.

A Collapsed Well

When a well collapses due to heavy rain or an earthquake etc., dirt and other impurities can enter your water supply, blocking and blackening your whole house water filter.

Finding the Source of the Problem

Taking care of the core problem will prevent your whole house filter from becoming black with tainted water. To that end, here are some things you can do to figure out the root cause of the problem:

Obtain a Water Test

water glass with sediment

The first step to determining the culprit is to have your water analyzed. It is a good idea to check your water for iron and manganese, as these minerals are common causes of black water/filters. However, several other types of tests are available depending on what you suspect might be the issue.

You can hire a professional to test your water or buy a do-it-yourself testing kit from a hardware shop.

Examine Your Well

Check your well to determine if the water level has dropped. When your well is short on water, it could allow sediment to enter your home’s water supply as they leak in from the ground.

Examine Your Septic System

A professional should inspect your septic system at least once a year to verify that it is in good working order.

Examine Your Pipes

Keep an eye out for corrosion in your pipes. Corrosion and rust are common problems with iron pipes. Have them inspected and repaired if necessary.

Examine Your Water Heaters

Corrosion is also a common issue with water heaters. Make sure to inspect yours!

Examine Your Water Filter Configuration

If you use a carbon filter in your whole house water filtration system and notice your water is black, the filter might need to be replaced. A filter that’s leaking media, or that has a lot of sediment build up, needs immediate changing.

How to Keep Your Whole House Water Filter from Turning Black

The blackening of your whole house water filter itself is sometimes unavoidable. However, you can take certain steps to reduce the frequency of these occurrences, such as:

  • Your whole house water filter should be replaced every 3 to 12 months, depending on how often you consume water and how dirty your water is.
  • Have your well water tested regularly.
  • Have your septic system and plumbing system inspected regularly.
  • Make a habit of regularly cleaning your water filtration system to reduce pollutant buildup.

If you take these precautions, you will be significantly less likely to experience a blackened and unsafe whole house filter.

Whole House Water Filter Maintenance

If your whole house water filter is the source of the black water, the best thing to do is replace it. This way, your water quality may be improved, and any health risks can be avoided.

Nonetheless, if you have verified that the cause is not hazardous, here are some suggestions for maintaining your whole house water filter instead of replacing it:

  • Replace the pre-filter if your main water filter is clogged.
  • Backwash the system more frequently if there is too much sediment in your water.
  • Another alternative is using clean water to flush your system, though this is not a guaranteed solution.


Your whole house water filter could turn black due to iron, manganese, black sediment or other filter stages (in the case of activated carbon filters) among other things.

You should have your water tested and check your home’s entire water system to pinpoint the reason.

Once you’ve figured out the problem, you can either apply the proper maintenance steps or contact a professional to assist you.

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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