Brown Water from Well: 5 Causes and How to Fix Each One

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Nothing is more alarming than turning on your faucet and seeing brown, murky water flowing out. If you have well water that’s suddenly turned brown, orange, or rust-colored, you’re probably worried about safety, and you definitely want it fixed fast.

The good news? Brown well water is usually caused by treatable issues, and most cases don’t pose serious health risks. The key is identifying the cause so you can apply the right solution.

I’ll walk you through the five most common reasons well water turns brown, how to identify which one is affecting your water, and exactly what to do to fix it. Whether it’s iron, sediment, tannins, or another issue, you’ll know how to get your water clear again.

Is Brown Well Water Safe to Drink?

Short answer: It depends on the cause.

Generally safe (but unpleasant):

• Iron contamination
• Manganese
• Sediment
• Tannins

Potentially unsafe:

• Surface water infiltration (after flooding)
• Sewage contamination
• Chemical spills nearby

When to worry: If brown water appears suddenly after:

• Heavy rain or flooding
• Well work or pump replacement
• Construction or excavation nearby
• Changes in water taste or smell

Always test your water if you’re unsure. A basic test costs $50-150 and gives you peace of mind.

Quick Diagnostic: Identify Your Problem

Before we dive into causes, let’s figure out what you’re dealing with:

The Glass Test

1. Fill a clear glass with brown water
2. Let it sit undisturbed for 1 hour
3. Observe what happens

Results:

Sediment settles to bottom, water clears: → You have sediment (sand, silt, or rust particles)

Water stays brown/orange, no settling: → You have dissolved iron or manganese

Brown tint remains, slight yellow/tea color: → You likely have tannins

Water clears quickly (5-10 minutes): → Air in pipes or recent disturbance

The Timing Test

When does brown water appear?

• First thing in morning: Iron bacteria or stagnant water
• After not using water for hours: Iron oxidizing in pipes
• Only from hot water: Water heater issue
• After heavy rain: Surface water infiltration or disturbed sediment
• All the time: System-wide contamination

The Location Test

Which faucets have brown water?

• All faucets, hot and cold: Well water problem
• Only hot water: Water heater issue
• One fixture only: Pipe corrosion in that line
• Outdoor faucets worse: Sediment in outdoor lines

Now let’s identify and fix the specific cause.

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Cause #1: Iron in Your Well Water

Likelihood: Very High (most common cause)
Safety: Not harmful, but ruins fixtures and laundry
Fix Difficulty: Moderate
Cost: $650-2,500

The Problem

Iron is the most common cause of brown well water. When iron levels exceed 0.3 ppm (parts per million), your water turns brown or orange and leaves rust stains on everything it touches.

Two types of iron:

Ferrous iron (clear water iron):

• Dissolved in water, invisible when first drawn
• Water appears clear from tap
• Turns brown/orange after exposure to air
• Easier to remove

Ferric iron (red water iron):

• Already oxidized, visible immediately
• Water looks brown/orange coming out of tap
• Has already reacted with oxygen
• Requires more aggressive treatment

Typical iron levels in wells: 0.5-10 ppm (EPA recommends under 0.3 ppm)

How to Confirm

Signs of iron:

• Orange/brown stains on toilets, sinks, tubs
• Rust stains on laundry
• Metallic taste
• Water clears when you let it sit (ferrous iron oxidizes)

Test your water:

• Home iron test kit: $15-30
• Professional lab test: $50-150
• Reveals exact iron concentration

The Solution

Treatment depends on iron level:

Light iron (0.3-3 ppm):

• Water softener (if ferrous iron only)
• Catalytic carbon filter ($600-1,200)
• Manganese greensand filter ($800-1,500)

Moderate iron (3-7 ppm):

• Air injection oxidation system ($1,500-2,200)
• Chemical oxidation + filtration ($1,200-2,000)

Heavy iron (7-15 ppm):

• Multi-stage oxidation system ($1,800-2,500)
• Professional chlorination + filtration ($2,500-4,000)

Our recommendation: 5 Best Iron Removal Systems for Well Water

Quick temporary fix: While saving for a filtration system, let water run for 2-3 minutes before use. This flushes oxidized iron that’s been sitting in pipes.

Prevention

Once you install treatment:

• Test water annually
• Maintain filters on schedule
• Replace media every 5-7 years
• Monitor for iron bacteria (creates slimy buildup)

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Cause #2: Sediment and Rust Particles

Likelihood: High
Safety: Generally safe, but indicates system issues
Fix Difficulty: Easy to Moderate
Cost: $50-800

The Problem

Sediment causes cloudy, brown water that settles when left standing. This includes:

Sand and silt:

• From well aquifer
• Indicates damaged well screen or casing
• More common in shallow wells

Rust particles:

• From corroding pipes or well casing
• From aging pressure tank
• From water heater deterioration

Mineral deposits:

• Calcium carbonate
• Manganese dioxide
• Other minerals breaking loose

How to Confirm

The glass test (described above):

• Fill glass with brown water
• Particles settle to bottom within 1 hour
• Water above sediment becomes clear

Check these sources:

• Drain pressure tank → Brown sediment comes out
• Flush water heater → Rusty water appears
• Check age of well and pipes

The Solution

Immediate fixes:

1. Flush your system:

• Open outdoor spigot (lowest point)
• Let water run for 15-30 minutes
• Repeat until water runs clear
• Cost: $0

2. Install sediment filter:

• 5-20 micron whole house filter
• Installed at point water enters home
• Catches particles before they reach fixtures
• Cost: $100-300 for basic system
• Filter replacements: $20-50 every 3-6 months

3. Clean or replace pressure tank:

• If tank is old and rusty inside
• Professional replacement: $400-800
• Extends life of entire system

Long-term solutions:

For well problems:

• Professional well inspection ($150-300)
• Well rehabilitation or screen repair ($500-2,000)
• New well (if severe): $5,000-15,000

For pipe corrosion:

• Whole house filtration to prevent further corrosion
• Pipe replacement if severely damaged
• Water treatment to adjust pH (prevents corrosion)

Recommended systems:

• Best Whole House Water Filters for Well Water
• Start with sediment pre-filter, then add carbon filtration

Prevention

Protect your well:

• Maintain proper well cap (keeps surface water out)
• Inspect well casing annually
• Address problems promptly
• Don’t over-pump well (causes sediment disturbance)

Protect your pipes:

• Install whole house filter
• Treat corrosive water (pH under 6.5)
• Replace aging galvanized pipes
• Maintain water softener (if you have one)

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Cause #3: Tannins (Organic Matter)

Likelihood: Moderate (common in certain regions)
Safety: Harmless but unpleasant
Fix Difficulty: Moderate
Cost: $800-2,000

The Problem

Tannins are organic compounds from decaying vegetation that give water a yellow, brown, or tea-colored tint. Unlike iron, tannin water doesn’t clear when sitting.

Common in:

• Areas with lots of surface vegetation
• Swampy or marshy regions
• Shallow wells near wetlands
• Wells in forested areas
• Southeastern United States

Characteristics:

• Water looks like weak tea or coffee
• Color doesn’t settle out
• Leaves yellowish stains
• Earthy or musty taste
• More noticeable in hot water (concentrates when heated)

How to Confirm

Visual test:

• Fill white container with water
• Compare to clean water
• Tannin water = yellow/brown tint throughout
• Doesn’t settle or clear when sitting

Bleach test:

• Add 2-3 drops bleach to glass of brown water
• If color disappears → Tannins
• If color remains → Iron or manganese

Professional test:

• Lab can measure tannin levels
• Also rules out other causes

The Solution

Tannin removal requires specific treatment:

Option 1: Anion Exchange System

• Works like water softener but removes tannins
• Requires salt for regeneration
• Effective for moderate tannin levels
• Cost: $800-1,500

Option 2: Activated Carbon Filtration

• Special high-grade activated carbon
• Removes tannins + improves taste
• Needs more frequent replacement than standard carbon
• Cost: $600-1,200

Option 3: Chlorination + Carbon Filtration

• Chlorine injection oxidizes tannins
• Carbon filter removes chlorine and tannins
• Most effective for heavy tannin levels
• Cost: $1,500-2,500

Option 4: Reverse Osmosis (point-of-use)

• For drinking water only
• Under-sink system
• Removes 95%+ of tannins
• Cost: $200-600

Not effective for tannins:

• Standard water softeners (don’t remove tannins)
• Basic sediment filters
• Standard carbon filters (need high-grade)
• Iron removal systems

Prevention

Once treated:

• Maintain system per manufacturer schedule
• Replace media/filters on time
• Monitor well for increases in tannin levels
• Consider well relocation if problem worsens

Well location matters:

• New wells should avoid marshy areas
• Deeper wells have fewer tannins
• Proper well construction keeps surface water out

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Cause #4: Manganese Contamination

Likelihood: Moderate (often occurs with iron)
Safety: Not harmful at typical levels
Fix Difficulty: Moderate
Cost: $800-2,200

The Problem

Manganese causes black or dark brown water and stains. It often occurs alongside iron, making water treatment more complex.

Characteristics:

• Black, brown, or purple stains
• Metallic taste
• Water may appear black when very concentrated
• Often found with iron

EPA secondary standard: 0.05 ppm (levels above cause staining)

Health note: High levels (over 0.3 ppm) may affect neurological development in infants. Test if you have young children.

How to Confirm

Visual signs:

• Black or dark purple stains (not orange like iron)
• Stains on fixtures, especially where water sits
• Dark sediment in toilet tanks
• Metallic taste stronger than with iron alone

Testing:

• Professional test reveals manganese levels
• Often tested together with iron
• Important to know concentration for proper treatment

The Solution

Treatment similar to iron but requires oxidation:

Light manganese (under 0.5 ppm):

• Water softener (removes some manganese)
• Manganese greensand filter ($800-1,500)
• KDF filter ($600-1,200)

Moderate to high (0.5-3 ppm):

• Air injection oxidation system ($1,500-2,200)
• Chemical oxidation + filtration ($1,800-2,500)
• Must treat iron simultaneously

Very high (over 3 ppm):

• Professional chlorination system
• Multi-stage filtration
• May need continuous treatment
• Cost: $2,500-4,000

Combined iron + manganese: Most systems that remove iron also handle manganese, but verify the specifications:

• SpringWell: Up to 1 ppm manganese
• Crystal Quest: Up to 3-5 ppm manganese
• See our iron removal system reviews

Prevention

After treatment:

• Regular filter backwashing (if applicable)
• Media replacement every 5-7 years
• Annual water testing
• Monitor for bacteria (can increase manganese)

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Cause #5: Surface Water Infiltration

Likelihood: Lower, but serious when it occurs
Safety: Potentially dangerous (bacteria risk)
Fix Difficulty: Requires professional help
Cost: $500-5,000+ depending on cause

The Problem

Brown water appearing suddenly after heavy rain or flooding may indicate surface water entering your well. This is serious because surface water can carry:

• Bacteria (E. coli, coliform)
• Parasites
• Chemicals (pesticides, fertilizers)
• Sewage contamination

Common causes:

• Damaged or missing well cap
• Cracked well casing
• Improper well construction
• Flooding overwhelming well seal
• Nearby septic system failure

How to Confirm

Warning signs:

• Brown water appears after rain
• Never had brown water before
• Sudden onset (not gradual)
• Water smells different (earthy, septic, chemical)
• Nearby flooding or water pooling

Immediate action:

1. Stop using water for drinking/cooking
2. Use bottled water
3. Test for coliform bacteria ($30-50)
4. Call well professional for inspection

The Solution

Step 1: Stop using contaminated water

• Bottled water for drinking/cooking
• Avoid bathing in severely contaminated water
• Don’t give to pets

Step 2: Identify entry point

• Professional well inspection ($150-300)
• Camera inspection of casing
• Pressure test of seal
• Check well cap and vent

Step 3: Fix the source

Well cap replacement:

• Cost: $50-150
• DIY possible
• Prevents surface water entry

Well casing repair:

• Cost: $500-2,000
• Professional required
• Seals cracks or damage

Well rehabilitation:

• Cost: $500-1,500
• Cleans and disinfects well
• Removes accumulated sediment

Grading and drainage:

• Cost: $500-3,000
• Directs water away from well
• Prevents future infiltration

Step 4: Disinfect well

• Shock chlorination ($200-400 professional, $50 DIY)
• Kills bacteria
• Flushes contaminants
• Retest water after 2 weeks

Step 5: Install protection

• Whole house filtration system
• UV sterilization ($200-800)
• Kills 99.9% of bacteria
• Backup protection

Prevention

Protect your well:

• Maintain proper well cap (sanitary seal)
• Inspect well annually
• Keep area around well graded away
• Maintain 50+ feet from septic system
• Don’t store chemicals near well
• Fix problems immediately

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When to Call a Professional

Call immediately if:

• Brown water appears suddenly
• Water smells strange (rotten eggs, sewage, chemical)
• Recent flooding in area
• Never had brown water before
• Pregnant women, infants, or immunocompromised in household

Schedule professional help for:

• Testing and diagnosis (if unsure of cause)
• Well inspection and repairs
• Whole house system installation
• Persistent problems after DIY attempts
• Iron levels over 10 ppm
• Any safety concerns

DIY is appropriate for:

• Installing sediment filters
• Basic system flushing
• Regular filter maintenance
• Monitoring and testing

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Cost Summary: Fixing Brown Well Water

CauseDIY CostProfessional CostTimelineIron (light)$600-1,200$1,000-2,0001-3 daysIron (heavy)$1,500-2,000$2,000-3,5003-5 daysSediment$50-300$200-800Same dayTannins$600-1,200$1,000-2,5002-4 daysManganese$800-1,500$1,500-2,5002-4 daysSurface waterN/A (requires pro)$500-5,0001-2 weeks

Testing costs:

• Home test kit: $15-50
• Professional lab test: $50-150
• Comprehensive analysis: $150-300

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Prevention: Keep Your Water Clear

Annual maintenance:

• Test water quality ($50-150)
• Inspect well cap and casing
• Check pressure tank for sediment
• Replace filters on schedule
• Monitor for changes

Protect your well:

• Proper well cap (sanitary seal)
• Grade area to drain away from well
• Keep 50+ feet from contamination sources
• Don’t over-pump (disturbs sediment)
• Professional inspection every 3-5 years

Maintain treatment systems:

• Follow manufacturer maintenance schedules
• Replace filters/media on time
• Backwash oxidation systems regularly
• Keep records of maintenance

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Frequently Asked Questions

Q: Can I still shower in brown well water?
A: If it’s iron or sediment, yes – though it may stain. If it’s from surface water infiltration or you smell sewage, no. When in doubt, test first.

Q: Will a water softener remove brown color?
A: Only if it’s caused by ferrous iron under 2-3 ppm. Softeners don’t remove ferric iron, sediment, tannins, or manganese effectively.

Q: How long does it take to fix brown water?
A: Simple solutions (sediment filter): same day. Iron removal system installation: 1-3 days. Well repairs: 1-2 weeks including retesting.

Q: Should I drink brown well water?
A: Not until you know the cause. Iron and sediment are generally safe but unpleasant. Surface water contamination can be dangerous. Test first, then decide.

Q: Why did my water suddenly turn brown?
A: Sudden changes indicate: recent well work, nearby construction, heavy rain/flooding, pump problems, or pipe corrosion. Investigate immediately.

Q: Can brown water damage my appliances?
A: Yes. Iron and sediment shorten the life of water heaters, washing machines, and dishwashers. Treatment systems protect your appliances and can save thousands in replacement costs.

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Your Action Plan

If you have brown well water right now:

1. ✅ Stop drinking water until cause is identified
2. ✅ Do the glass test (let water sit 1 hour)
3. ✅ Check when brown water appears (timing test)
4. ✅ Test your water (home kit or lab)
5. ✅ Identify cause using this guide
6. ✅ Choose appropriate solution
7. ✅ Install treatment or call professional
8. ✅ Retest water after treatment

For long-term clear water:

• Install whole house filtration appropriate for your problem
• Maintain system per schedule
• Test water annually
• Address problems immediately
• Keep well properly maintained

Recommended reading:

• 5 Best Iron Removal Systems for Well Water – If iron is your problem
• 7 Best Whole House Water Filters for Well Water – For comprehensive treatment
• Well Water Smells Like Rotten Eggs – If you also have odor issues

Brown well water is fixable. Identify the cause, choose the right treatment, and you’ll have clear, clean water throughout your home.

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Related Articles:

• Best Iron Removal Systems for Well Water
• Best Whole House Water Filters for Well Water
• Well Water Smells Like Rotten Eggs? Here’s the Fix