Toilet Not Clogged but Not Flushing Properly Fixed!

Last Updated on March 16, 2022 by toilethaven

Why Won’t My Toilet Flush but Isn’t Clogged?

Gravity flush toilets depend on gravity to dump a large volume of water in the bowl within a very short time in order to create a strong flush. It is the action of dumping a large volume of water in the bowl that creates the siphon effect which evacuates waste from the bowl.

In order for water to flow from the tank to the bowl within the shortest time possible, the flush valve, rim holes and siphon jets need to be fully open. You also need to have the correct level of water inside the tank.


If your toilet is not clogged but won’t flush all the way, it is a sign that that the siphon jet and rim holes are clogged, or the level of water inside the tank is too low. The problem could also be caused by a bent/warped flush valve, slack lift chain or a poorly designed drainpipe.

If you live in an area with hard water, a clogged siphon jet and rim holes are usually the culprit. This is especially caused by calcium deposits, commonly known as limescale.

If you are dealing with a new toilet that is not flushing all the way, you most likely have a poorly designed drainpipe. A toilet drainpipe needs to be sloping downwards to allow the waste to be evacuated from the bowl easily via gravity.

A toilet flapper is the rubber piece at the bottom of the tank that seals over the flush valve. It is connected to the lift chain which is in turn connected to the flush handle via the handle arm.

The lift chain should not be too slack otherwise it will not lift the toilet flapper all the way, meaning less water than intended will enter the tank. This will in turn result in a weak flushing toilet.

A warped or bent toilet flapper means that water will slowly seep underneath it and enter the bowl, reducing the water available for flushing. Again, this will result in a toilet that won’t flush all the way.

Now let us look at why your toilet won’t flush all the way and is not clogged in more details.

1. Clogged Siphon Jet and Rim Holes

When you pull the toilet flush handle down, the lift chain lifts the flapper out of the flush valve opening allowing water to flow down to the bowl. Water enters the bowl through the siphon jet and rim holes.

A siphon jet is a hole at the bottom of toilet bowl straight opposite the drain opening. It pushes a large amount of water down the toilet’s P-trap, to help create a stronger siphon, which is what helps in flushing.


Not all toilets have a siphon jet.

Rim holes are tiny holes located all around the rim of the bowl. In toilets with siphon jets, rim holes are used to rinse the bowl but those without siphon jets use water from these holes for flushing too.

You can easily see these rim jets if you hold a small mirror just underneath the rim of the toilet bowl like shown in the image below.


Modern toilets like Toto toilets which use the Tornado/double-cyclone flushing systems only have 2 holes/jets on the rim of the bowl, but they too could get clogged.

Most of the time when your toilet drain is clogged but the toilet won’t flush all the way, either the siphon jet, rim holes or both are clogged by mineral deposits. They could either be partially or fully clogged.

Clogged rim holes and siphon jet means that no water or very little of it enters the bowl from the tank during the flushing cycle. As I had mentioned earlier, you need a large volume of water to be dumped inside the bowl very fast to generate a decent flush.

To fix this problem, you will only need to unclog the siphon jets and holes. This is easier that unclogging a toilet drain.

How to Unclog Toilet Siphon Jet and Rim Holes

For this task you will need the following:

  • White vinegar
  • A small L-shaped wrench
  • Nylon gloves
  • A thin hose (optional)
  • Baking soda (optional)

After gathering together all the necessary items, it is time to get down to business.

  • Start by locating the siphon at the bottom of the bowl.
  • Wear the gloves and try to feed the thin hose through it in an attempt to unclog it. If you do not have the hose, push your finger inside it and try to remove as much calcium as possible.
  • Flush the toilet and check if the flushing power has increased. If it has, you have found the source of your problem. What you need to do next is to remove all the calcium deposits.
  • Use a plunger to force as much water as possible out of the bowl. Alternatively, soak it up using a cloth until the bowl is completely empty.
  • Remove the toilet tank lid and place it away. Make sure you place it in safe place where it can’t fall and break.
  • Carefully pour the vinegar down the overflow tube (about 2 cups of it). The overflow tube is the large tube inside the toilet tank.
  • Since the vinegar will find its way to the bottom of the bowl, you can also pour a cup of baking soda to quicken the breaking down of the limescale.

The vinegar will soak up the calcium in the siphon jet and rim holes thereby fully opening them. Some people opt to use muriatic acid but it is not good for the toilet finish, the environment and people on septic systems.

  • Wait for about 3 hours or overnight if you have the time.
  • Use an Allen wrench to poke through each rim hole to make sure that they are all open.
  • Flush the toilet and check if it is flushing as strongly as it should.

And basically that is how to unclog a toilet’s siphon jet and rim holes. To avoid this problem in the future, it is always a good idea to pour some vinegar or dish soap down the overflow tube from time to time.

2. Low Water Level in the Toilet Tank

The water level in your toilet tank should be about ½-inch below the overflow tube. If it is more than that, the extra water will flow down to the bowl via the overflow tube and hence a leaking toilet.

When the level of water in a toilet tank is too low, the toilet will not generate the required siphon during the flushing cycle meaning that it will not flush all the way despite it not being clogged.

Low water level inside a toilet tank also means low water level at the bottom of the toilet bowl. This is because there is a small tube (refill tube) connecting the fill valve to the overflow tube.

As the fill valve fills the tank with water, the refill tube sends a small amount of water down to the bowl via the overflow tube.

To adjust the level of water inside the toilet tank, you will need to adjust the toilet float. Toilet floats regulate the opening and closing of the fill valve by moving up and down the tank relative to the level of water.

This is how to adjust the water level in a toilet tank:

  • Check if you have a float ball (ballcock) or a float cup. Ballcocks are found in old toilets and as their name implies, they have a balloon-like ball connected to the fill valve using an arm. Float cups are small in size and are connected alongside the vertical body of the fill valve.
  • If you have a float ball, check where the float arm/lever connects to the fill valve. You will see a small screw. Use a screwdriver to slowly turn the screw clockwise until the water level is just about ½-inch below the top of the overflow tube.
  • If you have a float cup, look for a long plastic screw alongside the fill valve. You can use your bare hand or screwdriver to turn the screwdriver clockwise to increase the water level inside the toilet tank.

With the new water level in the tank, flush the toilet and check if it is flushing strongly again.

3. Warped or Bent Toilet Flapper

Although toilet flappers can last for a long time, they can warp or bend, which means they will cease creating the tight seal they are designed to do on top of the flush valve. When that happens, water will slowly leak from the tank to the bowl.

Mineral deposits underneath the flapper can also cause this problem. Insufficient water in the tank as we have seen results in a weak flushing toilet.

At times when the water level in the tank drops below the fill valve kick-in level, the toilet tank will start to refill on its own. This is the phenomenon mostly referred to as ghost flushing.

Unless you have mineral deposits under your flapper which you can easily clean, a warped or bent toilet flapper will need a replacement.

Replacing a toilet flapper is both easy and cheap if you are doing it for yourself. I have written a detailed guide on the same. Read it here.

4. Slack Lift Chain

For a decent flush, your toilet’s lift chain needs to have ½-inch slack. If it is too slack, it will not lift the flapper all the way up during flushing, meaning less water will flow to the bowl.

Another problem with a lift chain is that it could disconnect from the lever or flapper. At times, it can even get hooked to another toilet tank part limiting its movement.

Toilet lift chains rarely have problems but when they do, they are not easy to find since you don’t even think about them. Fix the lift chain if it is the culprit.

5. Poorly Designed Drainpipe

This problem only affects new toilets. If your toilet had decent flush power in the past and only deteriorated in the recent past then this will not apply to you.

A toilet’s P-trap helps in creating a siphon. After the P-trap, the drainpipe needs to be installed in a downward slope to help the waste quickly move out of the bowl.

Unfortunately, this is not a problem you can find out or fix on your own. You will need to hire a professional plumber to troubleshoot and fix it, meaning it will be quite expensive.

And basically that is how to fix a toilet that is not clogged but won’t flush all the way.