Why Is Toilet Flapper Leaking After Replacement? (6 Reasons!)

So, you have had enough of the constant noise and water leakage resulting from a faulty flapper and decided to replace it. However, to your surprise and disappointment, the toilet flapper leaking after replacement continues.

If replacing the flapper doesn’t stop the leak, the toilet bowl is probably cracked, the T bolts are broken or loosened, the wax ring isn’t correctly sized, or the drain is clogged. Before getting another replacement flapper, confirm the cause of the leak to avoid wasting your energy, time, and money.

You cannot live with a constantly leaking toilet, so keep reading to discover the root cause and learn how to fix the problem permanently.

Why is my toilet flapper not sealing?

Toilet Flapper Leaking After Replacement (Reasons & Fix!)

 ReasonRecommended Solution
1.  Poor tank and bowl connectionTighten the bolts connecting the tank to the bowl.
2. Clogged drainUnclog the drain line.
Loose or broken flange cups or boltsTighten or replace the flange cups or bolts.
A cracked bowlUse a waterproof sealant to repair the crack or buy a new toilet.
5.Flange or wax ring problemReinstall the flange and wax ring, ensuring it’s the right size.
6.A weak or damaged floor under your toiletRepair the floor, then reposition your toilet

1. Clogged Drain

A clog in the drain line should be the first thing you check since that will cause the waste and water to stop flowing. Every time you flush a toilet with a clogged drain, the water will accumulate in one place, putting too much pressure on the wax ring.

Continued pressure will loosen the seal, causing leaks.


Clear the clogs in the drain line using a plumber’s snake or rod, hot water, or vinegar and baking soda. You can call a professional plumber if you aren’t comfortable doing this yourself. 

2. Poor Tank and Bowl Connection

If your toilet continues leaking after replacing the flapper and unclogging it, check the connection between the tank and the bowl. Two to three bolts and rubber washers secure the bowl and tank together.

Over time, the washers wear out, and the bolts loosen, causing the toilet to leak from the toilet tank and water accumulation around the base. Inspect the bolts to see if they are loosened.


If the bolts are loosened, tighten them with an adjustable wrench to turn them clockwise. If the toilet continues leaking after tightening the bolts, replace the washers to create a water-tight seal.

This project isn’t time-consuming, and a beginner can undertake it comfortably.

3. Loose or Broken Flange Bolts

Flange bolts, also called T bolts or closets, are found at the base behind the plastic cups. These bolts ensure your toilet stays securely in place, so they must be properly tightened and in excellent condition.

If the flange bolts are loosened or broken, the wax rings won’t get sufficient pressure, which could cause leaks. Inspect the bolts to diagnose this problem.


You can fix this issue within 10 to 20 minutes using an adjustable wrench and a flat screwdriver. With the tools in hand, here’s what to do:

  • Reposition the toilet for stability.
  • Remove the flange bolts’ plastic cap using the screwdriver, then test the tightness of the bolts.
  • Tighten the bolts with an adjustable wrench if they are loose. Don’t tighten them too hard to avoid cracking the porcelain.
  • Put the plastic cap back.

If the flange bolts spin freely even after tightening them, they are likely broken or striped and need to be replaced. Toilet flange bolts and caps (View on Amazon) are easily accessible and affordable.

Toilet flapper not sealing

4. A Cracked Bowl

While a crack in the toilet bowl rarely happens, it can occur and cause your toilet to develop leaks. Hairline cracks can be difficult to notice, so you must inspect your toilet carefully to see them.


While a cracked bowl may compel you to get a new toilet, you can use a waterproof sealant to repair a tiny crack. You will need a towel, a putty knife, and a sealant to get the job done.

You don’t need to be experienced in plumbing to fix this problem, and it will take 25 to 30 minutes to get it done, costing you about $10. Follow the steps below to seal a bowl crack:

  • Stop the water supply to your toilet, flush it and remove the water in the bowl.
  • Clean and dry the toilet bowl.
  • Apply the waterproof sealant to the cracked area, then spread it with a putty knife.
  • Allow it to cure based on the directions of the manufacturer.
  • Pour water into the bowl once the sealant dries to see if the crack has been fixed.
  • Restore the water supply by turning on the shut-off valve, then flush your toilet multiple times.
  • The base will remain dry if you successfully seal the crack.

You’ll need to replace the toilet if the crack is too big.

5. Flange and Wax Ring Problem

The flange and wax ring are inter-connected, so it’s better to look into both when troubleshooting a leaking toilet. Before checking the flange, ensure the wax ring is the right size and perfectly compressed around the toilet flange.

Your toilet will likely leak if you install the wax ring correctly or is poor in quality. It’s easy to buy the wrong wax ring if you don’t have the knowledge and experience in plumbing.

Nonetheless, here’s how to ensure you have the right wax ring:

  • Checking the Wax Ring Size

Detach your toilet from the bathroom floor and tilt it sideways to access the elbow neck (the opening at the bottom of the toilet). Measure the elbow neck’s width to determine the wax ring’s precise width.

Don’t use the size of the old wax ring because its shape might be distorted after long-term use, giving you the wrong size.

  • Checking The Wax Ring Thickness

You can either have the regular thickness or double thickness, and the beauty of it is that you don’t need to measure your wax ring to determine its thickness. All you have to do is observe the installation position of the toilet flange.

Go for a double-thickness wax ring if the toilet flange sits beneath the bathroom floor and regular thickness if it sits flush with the bathroom floor.

If you have the correct wax ring size and compression but the toilet is leaking, examine the toilet flange. The flange joins the drainpipe to the toilet with the wax ring placed between the toilet and flange to create a seal, preventing sewage water leakage.

The toilet flange must be secured to the bathroom floor using screws, and it shouldn’t sit too far below the finished floor as that could compromise its functionality.


  • Reinstall the flange and wax ring if installed wrongly, ensuring you position them correctly.

6. A Weak Or Damaged Floor Under Your Toilet

A weak or damaged floor makes the wax ring lose its tightness with the flange and toilet, depriving it of sufficient pressure to form a proper seal.


  • Fix your bathroom floor and reinstall the toilet correctly. Consider seeking out a professional plumber if you can’t handle this project.

Why Your Toilet Ghost Flushes After Replacing Flapper

A faulty or damaged toilet flapper is usually the main cause of ghost flushing. This issue arises when your flapper cannot form a proper seal, allowing the water to keep flowing into the bowl and triggering a ghost flush to prevent overflowing.

Typically, replacing the flapper resolves the issue, but if it persists, the toilet handle is likely warping and pulling the flapper. In that case, replace the handle for a long-lasting solution.

Kohler toilet flapper not sealing after replacement


1. How Do You Stop A Flapper From Leaking?

You can prevent your toilet flapper from leaking by replacing it because a damaged or worn-out flapper doesn’t form a proper seal. However, ensure you get the correct size, shape, and material.

Most toilets use 2-inch flappers, but fairly new models (manufactured in 2005 and after) may require 3-inch flappers. Flappers are made of hard plastic or all-rubber, with the latter a popular choice, and they can be used with oddly sized valves or those positioned at an angle.

2. Why Is My New Toilet Flapper Leaking?

Your new toilet flapper is leaking because the flapper valves may be defective or warped, the chain is too long or short, or the gasket has an issue. Additionally, the seat of the flapper valve must be smooth.

It’s paramount to ensure you have the right flapper for your toilet and install it correctly.

3. How Much Water Can A Leaky Flapper Waste?

A leaky flapper can waste as much as 200 gallons of water every day, depending on the severity of the leak.

Final Remarks

Troubleshooting a toilet flapper leaking after replacement requires patience and know-how, and I hope this post provides a useful guide. Find out the cause, carry out a DIY project to solve it, and make sure you don’t make mistakes and intensify the problem.

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