Why does my toilet bowl get black stains?

Three causes cover most cases: mold or mildew, manganese in the water, and slime from bacteria that feed on iron or manganese. Each one leaves a slightly different pattern.

### Mold and mildew

Mold needs moisture, and a toilet bowl is wet all day. EPA says there are many types of mold and none of them will grow without water or moisture. It also says mold may begin growing indoors when mold spores land on surfaces that are wet, and that molds come in many colors, both white and black.

The spots that stay damp are the ones that darken first. That means the waterline, the underside of the rim, and the area around the rim jets and seat hinges. EPA has a bathroom tip that fits: places that are often or always damp can be hard to maintain completely free of mold, and if mold in the bathroom seems to reappear, more ventilation and more frequent cleaning will usually keep it away or at least keep it to a minimum.

If you want the why behind how quickly it comes back, see why a toilet grows mold so fast.

### Manganese in the water

Manganese is a mineral found in some water supplies. EPA lists a secondary guideline of 0.05 mg/L for manganese. Its table says that above that level, water can show a black to brown color, black staining, and a bitter metallic taste. Secondary guidelines cover looks, taste, and smell, not health limits, and EPA describes them that way.

Virginia Tech Extension says manganese causes brownish-black staining, similar to the reddish-brown staining iron causes. It also notes that water with lower concentrations of these metals may still cause staining problems. So a stain can show up even when the water meets the guideline.

The City of Phoenix water quality report lists hardness, iron, and other aesthetic measures. For questions about your water, the report gives 602-262-6251, Monday through Friday, except holidays, from 8:00 a.m. to 5:00 p.m., or WSDCompliance@phoenix.gov. A private well is a different story, and a lab test is the way to know.

### Slime in the tank from iron or manganese bacteria

Lift the tank lid. Virginia Tech says bacteria that feed on iron and manganese do not pose a health risk to humans, but produce a red-brown (iron) or black-brown (manganese) slime in toilet tanks, water troughs, or other places where water stands. Penn State Extension says the bacteria use dissolved iron or manganese in groundwater to grow, and that they are typically considered more of a nuisance than a health hazard. Because this is a groundwater problem, it points mostly to private wells.

Check where the marks are, what they do when you scrub, and what else in the house looks similar. This is a quick diagnosis, not a lab result, so treat it as a strong hint.

• Mold and mildew tend to sit where things stay damp. Look under the rim, at the seat hinges, around the base, and in the tank if condensation collects there. Spots that spread over time are a hint.
• Manganese staining tends to follow the flow of water. Look for dark brown or black streaks below the rim jets or at the waterline, plus the same dark marks on sinks, shower floors, and the inside of the washing machine.
• Tank slime points to bacteria. Virginia Tech, Penn State, and the University of Georgia all describe slime in toilet tanks. The University of Georgia adds that a brown or black gelatinous or fluffy mass in the tank can be a sign of iron bacteria, and that if disinfectant is used in the tank this sign may not show up.
• Try the normal cleaner test. Scrub a small patch with your regular cleaner and a soft brush. Marks that wipe away easily lean toward surface growth or film. Marks that stay put after two rounds lean toward mineral staining.
• Look at the rest of the house. Dark stains on several fixtures point to the water. A single fixture that only stains near the rim points to the toilet.

One warning applies to mineral stains. Virginia Tech says iron and manganese stains are generally not easily removed by soaps and detergents, and that using chlorine bleach and alkaline cleaners may intensify the stains. So do not assume that more bleach is better.

Use the mildest method that works, follow the product label, and never combine cleaners. Here is a safe routine.

### Cleaning dark spots step by step

1. 1Ventilate the room. Open the door or window and run the exhaust fan.
2. 2Wear gloves and eye protection. EPA advises gloves and goggles when working with mold or strong cleaners, and says goggles without ventilation holes are recommended.
3. 3Check your maker's care sheet. Kohler says most toilet bowl cleaners are safe on vitreous china when used inside the bowl only, and that strong abrasive cleaners scratch and dull the surface.
4. 4Apply a toilet bowl cleaner as directed on the label. Brush the waterline, under the rim, and around the jets. Lower the water level first if the ring sits at the waterline, since diluted cleaner works less well.
5. 5Rinse, flush, and wipe any splashes from the seat, hinges, and floor.
6. 6Repeat once if needed, then stop and think about the cause.

### A safety note on bleach

EPA says the use of a chemical or biocide that kills organisms such as mold, chlorine bleach for example, is not recommended as a routine practice during mold cleanup. It also says never mix chlorine bleach solution with other cleaning solutions or detergents that contain ammonia because toxic fumes could be produced. And it says that dead mold may still cause allergic reactions in some people, so the mold must be removed, not just killed. In practice, that means scrubbing it off with the cleaner you chose, not letting a soak do the job.

### If the ring will not budge

If dark marks stay after repeat cleaning, treat it as a mineral stain. Kohler's guide lists dedicated rust-removal products for its toilets, and Kohler tells owners to use a commercial cleaner designated for the removal of hard water deposits on the rim holes and trapways. Follow the package. For the mineral side of the story, see why a toilet bowl turns yellow.

Look for slime, discoloration, and leaks. The tank is the part of the toilet most people never open, and it often holds the answer.

• Slime or a film. A red-brown or black-brown slime on the tank walls fits the iron or manganese bacteria described above. Wiping it off helps for a while, but the bacteria live in the water supply, so the slime tends to return. Virginia Tech says the fix for such bacteria is disinfecting the water supply system with shock chlorination, then filtering, which suits a private well and is a job for the well owner or a qualified well professional.
• In-tank cleaners. Kohler says not to use in-tank cleaners because they can seriously damage the flush valve or other working parts.
• Leaks and condensation. A tank that keeps water moving or a cold tank that sweats keeps the porcelain and lid damp, which mold likes. See why a toilet tank sweats, how to fix a running toilet, and leaky toilet causes besides the flapper.
• Slow refill. If the tank refills slowly, water sits longer in the bowl and tank. See why a toilet fills so slowly and why a tank is not filling.

### How do I keep black stains from coming back?

Keep the bowl and tank from staying wet and damp, and treat the water if minerals are the cause.

• Clean on a regular schedule. EPA says more frequent cleaning in bathrooms helps keep mold to a minimum. Weekly is a common habit, though that timing is my suggestion, not an EPA number.
• Run the fan and dry the room. EPA advises increasing ventilation by running a fan or opening a window. The CDC recommends keeping humidity no higher than 50% and using exhaust fans that vent to the outside.
• Fix leaks promptly. CDC says to fix any leaks in your home's roof, walls, or plumbing so mold does not have moisture to grow. EPA says that if wet areas are dried within 24 to 48 hours after a leak or spill, in most cases mold will not grow.
• Test the water if stains keep coming. Dark staining on many fixtures is a water question. Ask a licensed lab, or the city water office, about manganese and iron.
• Use the right cleaner. Skip abrasive scouring powders and steel wool, which scratch porcelain.

Call when the cause looks bigger than the bowl. That includes tank slime that keeps returning, dark stains at every fixture, black growth around the base of the toilet or on the floor, a musty smell, or any sign of a leak. EPA says that if a moldy area covers more than 10 square feet, or there has been a lot of water damage, you should consult EPA's guidance for larger jobs rather than treat it as a home cleanup. A leak at the base is worth checking right away, as covered in why a toilet leaks at the base.

If you would rather have someone look, HQ Plumbing & Air is licensed and insured and gives free estimates. Upfront pricing comes before any work starts, and 24/7 emergency service covers a leak that will not wait. Learn more about our residential plumbing services.