Whole House Water Filter Turns Brown (Top Causes & Fixes)

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There are a few possible reasons why your whole house water filter might turn brown.

We’ve shared these reasons, and how to fix them, in this guide.

📌 Key Takeaways:

  • A whole home water filter might turn brown due to normal contaminant buildup, or excess contaminants like iron, manganese, silt, or tannins.
  • You can find out the cause of your brown whole house water filter by testing your water for one of these problem contaminants.
  • Resolve brown water problems by installing a suitable pre-filter to protect your whole house water filter from staining.

🔎 Causes Of Brown Whole House Water Filter

Below, we’ve shared the most common causes of a whole house water filter turning brown.

Normal Contaminant Buildup

If your filter is old and needs replacing, it’s normal for it to look dirtier than when you first installed it.

An old filter is clogged with organic matter that could give it a gray or brown tinge. Brown coloration on an old filter just tells you that the filter has done its job in trapping contaminants in your water supply.

Check your user manual if you’re not sure exactly when your filter needs to be replaced.

Old and dirty water filter clogged with contaminants

Iron Or Rust

If your filter is brown but it’s still relatively new, or the brown stains are darker than you’d imagine for normal contamination, iron and rust are the most likely culprits.

There are a few different types of iron that have staining abilities:

  • Ferrous iron, which is usually invisible in water unless it comes into contact with oxygen
  • Ferric iron, which has a brownish-red color and stains appliances and fixtures
  • Iron bacteria, a combination of iron and bacteria that leaves thick, brown, slimy deposits

Homes with old water pipes are most likely to have iron due to rusting inside the plumbing system. When water flows through rusty pipes, it picks up rust flakes and carries them through the plumbing. If you notice water with flecks of brown from your cold water tap, you probably have a rust issue.

Most new homes don’t have iron pipes and are less likely to have issues with rusting.

Well water has a higher likelihood of containing iron than city water because wells get their water from underground aquifers. As water seeps through the earth to reach the aquifer, it comes into contact with rocks and soils containing iron, which leaches into the water.

Related: Well water turned brown? This is how to fix it

Iron bacteria in water


Tannins, organic compounds most commonly found in well water, are another cause of brown, orange, or yellow-tinged whole house water filters.

Tannins are released from decaying plant matter and organic material. They’re another contaminant that dissolves into water as it seeps through the earth. Tannins are also present in various surface water sources, such as lakes and rivers.

While tannins have no health effects, they give an unappealing tea-like, dirty water appearance and a bad taste and smell.

We’ve covered how you can remove tannins from well water in this post.


If your drinking water has iron, it might have manganese, too – and this naturally occurring element is another contaminant that turns your water brown.

Manganese is present in soils and rocks, and enters groundwater supplies as the water travels into the aquifer.

Again, low levels of manganese have no health effects, but the mineral gives water a distinctive brown or yellow appearance.

Learn more about manganese removal in this guide.

Yellow or brown well water


Various types of sediment, such as silt and soil, may also turn your water brown and stain your whole house water filter.

Sediment should be minimal, even in a well water system, because wells are designed to filter out large particles to prevent them from being drawn into the well pump. But if any of your well components are worn or damaged, excess sediment and silt may enter your water supply.

You’re most likely to have silty water if you live in an area with high levels of erosion. Land disturbances and local construction can also disturb the soil and cause silt to enter your well, causing water discoloration.

🧰 How to Resolve Brown Whole House Water Filter: Step-By-Step

To tackle the cause of your discolored water and prevent your whole house water filter from turning brown, follow these steps:

Step 1: Test Your Water

Start by testing your water supply to find out what is causing your water to turn brown.

A good water test will tell you which contaminants are present in your water, and whether they exceed public guidelines. Private laboratory testing will give you the most accurate results.

Water testing with tap score

Step 2: Make Regular Filter Changes

If testing shows you that your water doesn’t contain many contaminants to blame for brown water filters, you might just need to start replacing your filters more frequently.

If your water quality is slightly worse than average, or you use more water than the average person, your whole home water filter might not last as long as predicted by the manufacturer.

Most filters in a whole home system need to be replaced every 3-6 months on average.

Changing the filter of traditional whole house filter

Step 3: Install A Water Treatment System

The best way to tackle a brown water issue is to remove the contaminant that’s causing the discoloration.

Some popular water treatment systems for brown water issues are:

Sediment Filters

A dedicated sediment filter is a good way to prevent brown coloration of a filtration system caused by sediment.

There are two common types of sediment filter systems:

  1. Sediment cartridge filters
  2. Spin-down sediment filters

Spin-down filters are best for large particles, while cartridge filters remove smaller sediment particles. You should install a sediment filter before any other pre-filter stages in your water filtration system.

Here are the best cartridge and spin-down sediment filters reviewed by WFG.

Tannin Filters

If tannins are a major issue in your home, you need a tannin removal filter.

There are a few different options to remove tannins in water, including ion exchange systems and reverse osmosis filters. The most effective method is ion exchange, using an acrylic or styrene-based chloride resin.

Iron & Manganese Filters

There are a few different filter options for manganese and iron in water.

Some whole home well water filtration systems have dedicated iron/manganese removal cartridges, usually made from KDF and similar media.

For high levels of iron and manganese, you can use an air injection or chemical injection system, which will also reduce the risk of iron bacteria growth.

Read up on our reviews of the best water filters for iron.

Springwell water softener and iron filter well water treatment system

Water Softener Systems

A whole house water softener is the best solution for low-to-moderate levels of iron and manganese in your well system. Water softeners exchange minerals with an ion that doesn’t affect water quality (usually sodium).

To prevent discoloration of your later water filtration stages, you’ll need to install these systems at your home’s point of entry, upstream of any other filter system in your home.

These are the best water softening systems for well water to consider.

Step 4: Replace Old Pipes & Water Heaters

Removing contaminants like dissolved iron from your water may do nothing if you have old, rusty pipes and a corroded hot water heater.

In this case, the key to resolving brown water problems in your home is to replace rusted pipes and plumbing fixtures.

❔ Whole House Water Filter Turns Brown: FAQ

Why does my whole house water filter turn brown?

Your whole house water filter might turn brown due to normal gradual contamination, dissolved iron and manganese, rusty water, or various sediments.

Is brown water safe to drink?

Yes, brown water in your home is usually safe to drink – although that depends on the cause of the water discoloration. For instance, if your brown water is caused by iron or manganese, high levels of these contaminants could be dangerous. If sediment or tannins are responsible for your discolored water, it’ll likely be safe to drink no matter what.

How do you filter out brown water?

Depending on the cause, you can filter our brown water by installing a sediment or iron filter, using a water softener, or replacing rusted pipes and hot water heaters.

  • Brian Campbell
    President & CEO, CWS, CWR

    Brian Campbell, a WQA Certified Water Specialist (CWS) and Certified Water Treatment Representative (CWR) with 5+ years of experience, helps homeowners navigate the world of water treatment. After honing his skills at Hach Company, he founded his business to empower homeowners with the knowledge and tools to achieve safe, healthy water. Brian's tested countless devices, from simple pitchers to complex systems, helping his readers find the perfect fit for their unique needs.

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