Iron Bacteria in Your Well? That Orange Slime & How to Treat It

You lift the lid of your toilet tank and find something disturbing—a rusty, slimy, orange-brown goo coating the inside. Maybe you've noticed it clogging your faucet aerators, staining your fixtures, or giving your water a swampy smell. That disgusting slime has a name: iron bacteria. And while it's not as dangerous as it looks, it can cause serious problems for your well and plumbing system if left untreated.

What Are Iron Bacteria?

Iron bacteria are naturally occurring microorganisms that thrive by oxidizing dissolved iron (and sometimes manganese) in groundwater. As they metabolize iron, they produce a rusty, slimy deposit called a biofilm—that orange goo you're seeing.

These bacteria are incredibly common. They exist naturally in soil, surface water, and shallow groundwater throughout the world. They're not introduced by pollution or contamination—they're just part of the natural environment. The problem is when they colonize your well system.

Iron Bacteria vs. Iron in Water

It's important to distinguish iron bacteria from simple iron content:

• Dissolved iron causes orange/brown staining but no slime. Water may appear clear until exposed to air, then turn orange.
• Iron bacteria produce slimy, stringy, or gelatinous deposits. You'll see actual buildup in toilet tanks, pipes, and fixtures.

Many wells have both—iron bacteria love high-iron water because there's more for them to "eat."

Signs You Have Iron Bacteria

Iron bacteria create distinctive symptoms that are hard to miss:

How Iron Bacteria Get Into Wells

Iron bacteria are everywhere in the environment. They typically enter wells through:

• Well drilling: Bacteria on drilling equipment, in drilling water, or in the soil are introduced during construction
• Pump repairs: Any time the well is opened, bacteria can enter on equipment or hands
• Surface water infiltration: Damaged casing, inadequate seals, or flooding allows bacteria-laden surface water in
• Contaminated equipment: Pumps, pipes, or tools previously used in infected wells

Once introduced, iron bacteria establish colonies and multiply rapidly, especially in wells with:

• High iron content (more food for bacteria)
• Low water flow or stagnant zones
• Moderate temperatures (they thrive at 25-40°F above ground temperature)
• Oxygen exposure (they're aerobic)

The Damage Iron Bacteria Cause

While iron bacteria aren't a health threat, they cause significant practical problems:

"We've seen wells where iron bacteria completely clogged the well screen, reducing a 20-gallon-per-minute well to barely a trickle. The slime just keeps building until something fails."

In the Well

• Clogs well screen, reducing water flow
• Coats pump components, reducing efficiency
• Creates conditions for corrosion
• Can harbor sulfate-reducing bacteria that cause more severe odors

In Your Plumbing

• Builds up inside pipes, reducing diameter and flow
• Clogs water softeners, filters, and treatment equipment
• Stains fixtures, laundry, and dishes
• Accumulates in water heater, reducing efficiency and lifespan

Indicator of Larger Issues

• May indicate poor well construction or damage
• Can harbor harmful bacteria within the biofilm
• Suggests conditions that might allow pathogen entry

Testing for Iron Bacteria

Iron bacteria are often diagnosed visually—that distinctive slime is hard to mistake. However, laboratory testing can confirm the presence and identify the specific type:

• Visual inspection: Orange slime in toilet tank is often sufficient for diagnosis
• BART test (Biological Activity Reaction Test): Simple field test kit, results in 1-8 days
• Laboratory culture: Most accurate but takes longer, identifies specific bacteria types

How to Treat Iron Bacteria

1. Shock Chlorination (Most Common Treatment)

Shock chlorination involves introducing a strong chlorine solution into the well to kill bacteria. This is the most common and often effective first-line treatment.

The process:

1. Calculate required chlorine based on well depth and diameter
2. Mix chlorine solution (typically household bleach or calcium hypochlorite)
3. Pour solution into well
4. Circulate by running water back into well
5. Run chlorinated water through entire plumbing system
6. Let sit for 12-24 hours (longer is better for iron bacteria)
7. Flush system until chlorine smell is gone

Cost: DIY: $50-$150 in supplies. Professional treatment: $300-$600.

Effectiveness: Often provides temporary relief, but iron bacteria frequently return within months to a year. For persistent cases, ongoing treatment is needed.

2. Continuous Chlorination

For wells with recurring iron bacteria, continuous low-level chlorination can keep bacteria under control. A chlorinator automatically adds small amounts of chlorine to incoming water.

Pros:

• Ongoing protection against bacteria
• Also disinfects against other pathogens
• Oxidizes iron for easier filtration

Cons:

• Requires ongoing chemical purchases
• Need contact tank and filtration to remove chlorine taste
• More complex system to maintain

Cost: $1,000-$2,500 for system installation plus ongoing chemical costs.

3. UV Disinfection

Ultraviolet light systems kill bacteria as water passes through. While effective against bacteria in the water, UV doesn't eliminate established colonies in the well or pipes.

Best for: Preventing bacteria from reaching fixtures after other treatments have cleaned the well and system.

Cost: $500-$1,500 for system installation.

4. Well Rehabilitation

For severe infestations where biofilm has heavily colonized the well, simple chlorination may not penetrate the slime layer. Professional rehabilitation may be needed:

• Physical brushing and scraping of well casing
• High-pressure jetting to remove biofilm
• Acid treatment to dissolve iron deposits
• Surging and bailing to remove loosened material
• Heavy chlorination after cleaning

Cost: $2,000-$5,000 depending on well depth and severity.

DIY Shock Chlorination Guide

If you want to try shock chlorination yourself:

Preventing Iron Bacteria

Complete prevention is difficult since iron bacteria are so common, but you can reduce the risk:

• Insist on disinfection: Any time the well is opened (pump repair, etc.), have it chlorinated
• Maintain well integrity: Ensure casing and seal are in good condition
• Use clean equipment: Ensure any equipment entering the well is sanitized
• Consider preventive treatment: Periodic shock chlorination before problems develop
• Address iron: Iron removal treatment reduces "food" for bacteria

When to Call a Professional

Get professional help if:

• DIY shock chlorination doesn't work or bacteria return quickly
• Heavy biofilm buildup that may require physical removal
• Reduced well yield suggesting screen or pump clogging
• You're uncomfortable working with the well
• Coliform bacteria also present (indicates contamination path)
• You want to install ongoing treatment (chlorination or UV)

How SCWS Handles Iron Bacteria

At Southern California Well Service, our iron bacteria treatment includes:

1. Assessment: We inspect the well, test water, and evaluate the extent of contamination
2. Professional shock treatment: We use appropriate chlorine concentrations and methods for effective kill
3. System cleaning: We address pressure tanks, water heaters, and plumbing as needed
4. Well rehabilitation: For severe cases, we can brush, jet, and acid-treat the well
5. Ongoing treatment options: We can install chlorination or UV systems for lasting control
6. Follow-up testing: We verify treatment effectiveness

Frequently Asked Questions

Get Rid of That Orange Slime

Iron bacteria are a nuisance, but they don't have to take over your well and plumbing. With proper treatment—and sometimes ongoing maintenance—you can eliminate the slime, protect your equipment, and enjoy clean, clear water.

Whether you need a one-time shock treatment or want to discuss long-term solutions, we're here to help. Call us for a professional assessment and treatment plan.