What is actually growing in there
Iron bacteria is not one organism. It is a handful of naturally occurring genera, Gallionella, Leptothrix and Crenothrix among them, that make a living oxidizing dissolved iron and manganese. They take iron in its dissolved form, pull energy from oxidizing it, and dump the oxidized iron back out as a rusty sheath around themselves. Millions of them together are the slime you are looking at, mostly iron oxide wrapped in a sticky organic coat, which is why it is the color of rust and the texture of a neglected drain.
Start with the reassuring part. These are not pathogens. They do not cause disease, they are not regulated as a health contaminant, and a house that has had them for fifteen years has not been drinking anything dangerous. New Jersey's standard well panels do not test for them, because there is no health standard to test against. They are a nuisance organism, and the nuisance is real: taste, odor, staining, plugged equipment, and a well that quietly loses yield.
The complication is the company they keep. An iron bacteria biofilm is oxygen free on the inside, which happens to be exactly where sulfate reducing bacteria want to live. That is why an iron bacteria well so often smells swampy, musty, or like rotten eggs at the same time. The two problems travel together and they get treated together.
Iron bacteria, dissolved iron, or manganese
Three different things stain, and they get confused constantly, so sort yours out before you spend a dollar on equipment. Dissolved iron, sometimes called clear water iron, comes out of the tap clear and turns rust colored in the glass over ten or twenty minutes as it hits air. Oxidized iron, red water iron, arrives already orange and cloudy. Neither is slimy. Rub either between your fingers and you get grit, not gel.
Iron bacteria is the slimy one, and the tells are specific. Take the lid off the toilet tank, because that tank is the best window into your water in the house: still, dark, room temperature, continuously refreshed. If the walls and the flapper are coated in a soft reddish brown film that comes away in strings on your finger, you have a colony. An oily looking rainbow sheen on standing water is another tell, and there is a field test for it worth knowing. Poke it with a stick. A petroleum sheen swirls and flows back together. A bacterial sheen cracks into rigid plates like a broken windshield.
Manganese is the third one and it runs darker. Manganese staining is black, gray brown, or the color of coffee grounds. It shows as black specks in an ice cube, a black ring at the waterline in the toilet, and dark flecks off an aerator screen, and it stains at much lower concentrations than iron. The secondary standards tell the story: iron becomes a nuisance around 0.3 milligrams per liter, manganese around 0.05. A well that tests low for both and still stains and smells is telling you the problem is biological, and no softener fixes biology.
Log the other symptoms, because they narrow it fast. A filter cartridge that used to run six months and now plugs in six weeks. Slime you can feel inside a hose bibb or on a washing machine inlet screen. A slug of orange after the house sat empty. A smell that is worse first thing in the morning. That last pattern, worse after the water sits still, is biology almost every time.
What it does to a well and a pump
Left alone, iron bacteria does not stay in the toilet tank. It grows wherever the water is: out in the fractures feeding the well, on the casing wall, on the drop pipe, inside the pump, in the pressure tank, and through every foot of house plumbing. The mass builds slowly and the effects arrive all at once.
In the well itself, the biofilm plugs the same narrow fractures your yield depends on. A 5 gallon per minute well fouling for a decade can measure 2, and the homeowner is certain the pump is dying. In the pump, the sheath builds on the intake screen and inside the impeller stages, so it moves less water on the same amperage and runs longer and hotter to do it. In the pressure tank, sludge settles and breaks loose in slugs whenever the tank draws down hard, which is why the orange shows up on laundry day.
Downstream it is filters and appliances. Cartridge filters plug. Softener resin fouls and stops exchanging, and a softener killed by iron bacteria gets written off as a bad softener by people who never looked at why. Aerator screens fill. Toilet fill valves stick open. Water tests get strange too, because biofilm sloughing into a sample bottle can throw a total coliform hit and send a homeowner chasing a contamination problem they do not have.
None of it happens overnight, and that is the trap. The decline is slow enough that a family adjusts without noticing, and the call comes when the yield or the filter life finally crosses a line somebody cares about.
Shock chlorination, and what it will not fix
Shock chlorination is the first move and on a lot of wells it is the only one needed. It means putting a strong chlorine solution down the casing, circulating it back through the well and out to every fixture until you smell chlorine at each one, holding it twelve to twenty four hours, then flushing the system somewhere the chlorinated water will not kill a lawn or knock out a septic field. Done properly it kills the colony in the casing, the drop pipe, the tank and the house plumbing. It is an affordable service call, and often the first thing worth trying.
The reason so many homeowner shocks fail is dose, contact and time. A capful of bleach is not a shock. Killing an established biofilm takes hundreds of parts per million held for most of a day, not the couple of parts per million that sanitizes a clean well after a pump job. The chlorine also has to physically reach the slime, which means agitating the water column rather than pouring and walking away, and on a badly fouled well it means brushing or swabbing the casing wall first, because chlorine does not penetrate a thick sheath. Chlorine also disinfects better in neutral to slightly acidic water, and a lot of wells in this bedrock run acidic, which works in your favor.
Here is what a shock will not do. It will not reach out into the water bearing fractures. The colony lives in the rock beyond the borehole and no dose you pour down a hole treats the formation. It will not remove iron, because iron is chemistry and bacteria are biology, so a well with 3 mg/L of dissolved iron still has 3 mg/L the morning after a perfect shock. And it will not clean a fouled softener bed or a slimed filter housing, so those get serviced in the same week or they reseed what you just cleaned.
When the answer is a routine, not a cure
Now the honest part. Where the colony is established out in the formation, it comes back. Not always, and not always fast, but often enough that you should plan for it. The measurement that matters is how long the quiet period lasts. Gone for a year or more, and shocking once a year is a sane way to live with it, and plenty of our customers do exactly that every spring. Back in three weeks, and you have a continuous source that needs continuous treatment.
Continuous treatment means a small chemical feed pump wired to run with the well pump, a contact tank sized so the chlorine has time to work before the water reaches the house, and a backwashing filter or carbon tank after it to take out the oxidized iron and the leftover chlorine. Installed, it is a real investment, and the iron load and your plumbing decide where in the range you land. It is not a set and forget appliance. Somebody mixes solution, checks the residual and services the filter. Some systems feed hydrogen peroxide instead, which oxidizes faster and leaves no taste, at a higher cost per gallon.
Sequence matters as much as equipment. Clean the biology out first, then size filtration against a test taken after the well is clean. Do it backwards, hang a filter on a fouled well, and the new equipment becomes the colony's home inside a season. We have pulled out two year old systems that never stood a chance, because they were sized off a sample full of biofilm.
Set your expectations honestly. On a well that has it badly, iron bacteria is managed rather than cured. The goal is clear water, clean fixtures, filter media that lasts its rated life and a well that holds its yield. That is achievable and it is worth doing. A permanently sterile borehole is not a thing.
How it got in, and keeping it out
It is not native to deep rock the way dissolved iron is. It gets introduced, and the doors are predictable: an unsealed well cap, a cap below grade where runoff pools, surface water finding the annular space outside the casing, a flood, or unsanitized equipment going down the hole. A pump, a length of drop pipe or a rope laid on the dirt and lowered into a clean well can seed a colony that takes years to become visible.
That is why a competent pump job ends with disinfection every time, and why we keep pipe off the ground. It is also why the well cap deserves two minutes of your attention this weekend. You want a sealed sanitary cap with an intact gasket and a screened vent, a foot or more above grade, on a casing with no cracks, with the ground graded to run water away. A cap down in a buried pit with an inch of water in the bottom is an open invitation.
A lake lot or a low spot that takes water in a wet spring, or slime that showed up a year after the well was opened for a pump job, are the two histories we hear most. Shock it, close the entry point, then decide about ongoing treatment based on how long it stays gone. If you want a sample pulled at the wellhead, call 973-853-1550.