Hard Water Deposits in a Toilet Bowl

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Dear Home-Ec 101,

During the walk-through when we purchased our current home, we flushed our toilets but did not raise the lids. After we moved in, to our horror, two of our toilets were gross!

First problem, I am told that it is hard water deposits, so when toilet waste is flushed down, stuff catches on the way down. I have been able to remove what I can see after repeatedly cleaning. But there is still a smell. Second toilet, the bowl is black. Have tried a few cleaners, but with little results. Help!!
Down and Dirty in Delaware

ceramic frog sitting on a toilet with text how to get rid of hard water deposits in a toilet bowl

Heather says:

I do not envy your grungy toilet problem. Nope, not even a little bit.

Get yourself some rubber gloves. You know, the heavy-duty, no-nonsense, I’m about to use cleaners that mean business kind of gloves.

Now don’t worry, I’m not suggesting anything toxic, but acids, even those from non-toxic sources are not good for your skin. Ever cut a ton of citrus fruit and had your hands feel raw for a couple of days? It’s like that.

So get your gloves and either Bar Keepers Friend or your other favorite acidic cleanser.

Why acidic cleanser?

You’re going to be cleaning up some foul funk known as limescale and urine scale. You know where the limescale comes from -hard water- but the urine scale is a special treat all on its own. It forms from the ammonium salts left behind when urine splashes and evaporates.


I kid. Well, about the yum part, the urine scale is a fact of life, disgusting but we all have to deal.

You’re also going to want some kind of scrubber – a generic scrub brush or even one of those nylon kitchen jobbers, but know that you WILL BE THROWING THAT OUT AFTERWARD, right? You can, of course, wash and reuse the scrub brush, but please delegate it to the floors or bathroom use only.

Now turn off the water to the tank. (Righty tighty, lefty loosey)

Flush the toilet so there is no water in the bowl.

Put on your gloves, apply the cleanser to the bowl and give the inside a good scrub, as far down as you can reach and spend a lot of time up under the rim. (Many people forget to clean this area and all kinds of heinous funk can hide up here.) Don’t spend a lot of time with this scrubbing, you’re mostly just trying to make sure that the cleaner has gotten into every nook and cranny in the toilet bowl.

Now stand up, put the lid down on the toilet, take off your gloves, wash your hands, and set a timer for 30 minutes.

Go entertain yourself. Welcome back.

Remember when we’ve talked about how cleaning takes a few kinds of energy:

Thermal Energy

Not applicable or safe in this case – never, never, never pour hot water into your toilet, the thermal change can crack your bowl and that’s not fun for anyone. I don’t care what you read where on the interwebz. No. No. No. Got it?

Chemical  Energy

Your cleanser -and with chemical energy comes the need for time for those chemical reactions to take place, that’s why you left the room for a little while.

Physical Energy

Yup, here’s where you and the scrub brush come in.

Now, put your gloves back on, wet your scrubber, and go scrub the ever-living-snot out of that toilet bowl.

When you’re sure you’ve gotten as much as will come off this round, turn the water back on to the tank, and flush the toilet.

Flush it one more time and give it a little scrub with a standard toilet brush.

Flush again.

Now, leave the room for five minutes or so and come back and give the area a smell.

If it still smells funky, it’s not the bowl.

Turn the water back off. Empty the tank, and carefully remove it. (You’re going to have to disconnect the water line and undo a couple of bolts to do so).

Give the area that you couldn’t reach with the tank attached a thorough cleaning. Rinse, dry, give the area a little while to air out, and come back. Do you still smell the funk?

If so, it may be either urine or other filth between the flooring and toilet or the wax ring may need to be replaced. Be prepared for this job to turn into more, if there is water damage to the flooring and/or subflooring.

If you are a dude very strong, this could be a one person job. I’m not a wuss, but moving a ceramic toilet bowl is more than I can handle on my own—those suckers are HEAVY—so you may have to call in a friend or significant other for physical help with this job.

Please do not hurt yourself trying to move more than you should.

Loosen the bolts that attach the toilet to the floor. Move the toilet out of the area and clean the area up to the drain as thoroughly as possible. Use a cleaner that is safe for your flooring.

Inspect the wax donut -or since you already have the toilet moved, replace it, while you have it out of the way and save yourself a project 3 years from now.

bathroom cleaning
Tips to keep your bathroom squeaky clean!

Look for water damage that may indicate the seal was compromised. If there is damage, that may be the real source of your odor,  but that repair is out of the scope of Home-Ec 101.

Water damage to flooring is more of a Bob Villa, This Old House type job.

Hire out if you must. You can, of course, put the toilet back together until you can afford the repair, just be glad you know the source and make sure this repair is high on your list of MUST-DOs, as water damage doesn’t go away with magical thinking and gets worse while you ignore it.

If there is no water damage, put everything back together and enjoy your now funk-free bathroom.

Submit your questions to helpme@home-ec101.com.

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13 thoughts on “Hard Water Deposits in a Toilet Bowl”

  1. Pumic stones (not the same one you scrub your feet with) are a great tool for cleaning especially dirty toilet bowls. You can find them in the pool section of home depot or lowes and they work wonders! In my mind the big heavy duty gloves are in order any time I’m sticking my hand into the toilet bowl…

  2. I live in an area with super hard water. I clean our bathrooms with Arm and Hammer washing soda. Not baking soda….I love how it works. I use the pumic stone too on the toilets once a year or so…with regular cleaning the washing soda does a great job. I do wear gloves when my hands go into a toilet.

  3. The most important step is to get a water softener so you don’t have continued limescale buildup. If hard water is forming deposits on the toilet like that, it’s probably also causing problems in other parts of the house as well.

  4. I do the same thing, flushing the water and scrubbing for our hard water stains, but I use something that is called “cleaning screen” that a professional cleaner told me about. It is awesome! It comes in 12×10 inch -ish sheets, and is a stiff, thick screen material, similar to window screen. It has a grit and texture that will scrub hard water, soap scum, and anything else off of hard surfaces. I bought it at our local janitorial supply store.

  5. Wow I’m so glad I don’t have hard water build up on my toilets. The only thing I have to deal with is cleaning it 5 times a day because none of my children seem to be capable of wiping, GROSS. Nothing like pee ON the potty 🙂

    • I taught them how to do it, themselves. Solved the problem cuz they didn’t want to do the grunt gross work. .02

      I’ve also had to use a pumice stone before. IF you feel your toilets are already ruined, this can’t hurt it. My great grandmother taught me and it was kind of funny. I burned a pot. She said to bleach it. I said won’t that ruin it and she said “isn’t already ruined?” Great missed advice. Good luck. 🙂

  6. I use the same method as described. Howewer, sometimes I use Coke (it doesnt have to be CocaCola) and will leave it for a bout 1 hour. After that you will see the bowl will be cleansed once again.

    Anyway, thanks for sharing the above tip.

  7. Hi I have the same problem. But we are on a septic tank . So we cant flush any thing that will kill the micro bugs in the septic tank. I scrub as far as i can reach then about 5 years we have to install a new toilet. Because the old toilet clogs up in the trap where i cant reach. We tryed to snake it out but the snake broke because of the bend in the trap. We cant use a water softener because its salt. Any sugestions ?

    • Can you use vinegar? We have very hard water and when we get scrub resistant scale, I turn off the water, get the toilet as empty as possible ( flushing until it’s low and then pouring -quickly- about two gallons of water in works). Fill the toilet with cheap white vinegar to the water line and let it sit overnight. The acid loosens the bonds and you can use a toilet brush to scrub the next morning. Turn your water back on, flush and see a brand new loo! Our plumbing is connected to the city main so we have difference circumstances but it works so well you might want to look into it. Also, I have used vinegar to remove paint off old knobs for dressers, etc.

    • I have very very hard water and also have a septic tank, where I live it is mandatory to pump and inspect our septic every 5 years (I live in a protected area of the 2nd largest florida aquifer so its a public safety thing…fyi the entire state sits on limestone and our aquifers are made of limestone tunnels, as I sit directly on land that is at the water source, I have some of the highest levels in the state… lol hence the super hard water)

      If I did not do this method, I would have to replace my toilets probably every other year due to total blockage, as with shower heads and well, pretty much everything. Its a huge problem here. Plumbing is a nightmare and in truth this also helps my plumbing stay clear. The city recently came out and installed much larger than average piping in our whole area because we have such thick lime deposits even in our city water!

      …and so before I tell you what I do… please know, I really hate to do this, but the very very small amounts I use have not yet upset my septic balance in the 10+ years I have done this and I do NOT do this every toilet cleaning! (also for what it is worth, I use minimal amounts of non toxic biodegradable septic safe cleaners everywhere else, along with distilled water and my industrial steamer for cleaning to keep my footprint down and tank operational…we also do not flush any paper anything as it is harder on the septic to break down than waste, In our 2 inspections, my septic has been very very healthy) This is a maintenance thing so I dont get totally blocked. I do this around 3 to 4 times a year and quite frankly my plumbing needs it too. I drain the toilet as described, but I put a very thin, as little as possible, layer of the works toilet cleaner on all deposits, dont forget the holes where the water drains into the toilet, it contains HYDROCHLORIC ACID and this stuff is no joke, but will eat through months of build up in 30 minutes of soaking, with very little scrubbing needed. (I literally push it off with one swipe of the scrub brush) Ventilate well, very very very well. If you have a totally blocked up toilet you can save it, but I would recommend removing the toilet and doing this outside, and collect the acid after use into a HDPE type plastic container for proper disposal, due to the amount you would have to use, no water system should be processing this stuff…yet it is in this toilet cleaner, go figure. Its a double edged sword, using something this strong…but things like vinegar and even pumice are a joke here where I live. Its just too much scale too quick for these methods…unless you don’t mind replacing your toilets every other year of course or scrubbing by hand like that at least weekly, or even bi-weekly for best results…believe me, I tried for a while. I just don’t have 30-45+ minutes to dedicated to scrubbing and poking the build up out of my water inlet holes with nails, bamboo skewers, etc. these less effective removers twice a week per each toilet in my house. I have so many other hard water issues to deal with in my washer, inlets, sinks, shower heads, etc. to do that.

      So, for what it is worth…this is what I have unfortunately had to resort to but it does work, and it works like nothing else mentioned here. I really wish I had a better answer…that is how I found myself here today…always looking for a better way. Unfortunately these suggestions just are not strong enough for my water conditions.

  8. What about distilled white vinegar? I use this all the time to remove hard water scale on sinks, showerheads etc. For the toilet you could drain out the water, fill it up with vinegar, let it soak overnight, and lightly clean it with a brush in the morning.

    • With mine, the scale is high up, so the vinegar doesn’t sit on it. I tried using ketscup (has vinegar and sticks). Didn’t work though. Tried soaking papertowels in it and squishing them against the area, but they just slide down soon after.

      I also tried pretty much everything else besides barkeeper. Coke, tang, CLR, The Works, borax, Kaboom, brillo, those plastic sponges, etc..

  9. I had dark scaly deposits at the bottom of my toilet. Nothing worked to remove it. I used vinegar, rust, lime calcium cleaner, a pearing knife, wire brushes etc. Finally I tried a small metal tooth plaque remover (from a local pharmacy – the pointed sharp curved type), and with a very small amount of elbow grease I was able to remove the deposit it one complete sheet. My plaque remover was pretty banged up but the tiny point was able to get underneath and shift it up. Looks new! So thrilled.


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