What To Do If Your 
Boat Exhaust Is Clogged

Boat Maintenance
Paul Luisi
by Paul

A clogged boat exhaust and exhaust manifold can cause your boat motor to overheat, stutter, cut out, create lots of smoke or even fail to start.

If the clogged exhaust is left untreated, it can result in serious engine damage or in some instances even a fire.

If you are getting an exhaust alarm or alert, either at idle or at wide open throttle, it could be a signal of the exhaust, the exhaust manifold, the elbow or riser being blocked and clogged up.

Poor boating environments or failure to clean the exhausts after some time can cause the boat exhaust to get clogged up with seaweed, dirt, sand, oils, grease, grime or other hard and pasty materials.

Ensuring the exhaust is clear from these materials is very important for the smooth running of your boat engine and also the fuel consumption of the watercraft.

To unclog a boat exhaust, follow the steps: 

  1. Check the exhaust system and identify the clogged areas
  2. Remove the exhaust manifolds from the boat
  3. Remove the dirt & clean the clogged exhaust
  4. Refit the cleaned exhaust system
  5. Start up the boat and check everything is operating correctly

These instructions apply to both wet marine exhausts and dry marine exhausts.

They will also ensure the exhaust is unclogged and should help the boat motor to run smoothly again.

1. Check The Exhaust System & Identify The Clogged Areas

Clogged Boat Exhaust
Clogged boat exhaust example

The first step is to check the boat exhaust area and identify the clogged areas in the exhaust system.

This is easier to do on an outboard motor where the exhaust is located at the base of the propeller compared to an inboard motor where gaining access to the exhaust manifold area may be more difficult.

To check the exhaust for clogging: 

  • Check for exhaust alarms or exhaust manifold warnings signals (where applicable): If there is an alert on your boat signaling exhaust issues, this can be a sign of clogging in the exhaust system
  • Visually inspect the external part of the exhaust: This is done by visually inspecting the external part of the exhaust to see if the most visible part of the exhaust system is clogged up with materials/dirt. If there is a clogged-up area on the surface, this can mean there is more clogging on the internal exhaust manifold area too
  • Check the exhaust manifold area: If there is no visible clogging on the surface, you will need to dig deeper and check out the exhaust manifold area for a build-up of dirt. Many times, the exhaust manifold area is clogged up with dirt that can not be seen on the surface

Once the clogged areas of the exhaust system are identified, it's time to get to work on unclogging it.

2. Remove The Exhaust Manifolds From The Boat Engine

The second step for unclogging a marine exhaust is to remove the exhaust manifolds and risers.

Removing the manifolds will help you to get the clogged-up dirt, grime and grease out from deep in the exhaust system.

Removing the exhaust manifold will depend on the brand and type of engine so a boat owner should follow the instructions in their boat engine manual.

Generally, to remove the exhaust manifold and unclog it, you will need tools like:

  • Gloves
  • Screwdrivers
  • Ratchets
  • Whiz Wheel
  • Torx Socket
  • Gasket Scraper
  • Bristle Brush
  • Cleaning Fluid
  • Bucket

As a pro tip, if you are struggling to get the elbows off and are afraid of breaking them, heat it with a torch which will help the elbow expand and make it easier to remove without damaging it.

Once the exhaust manifold is disconnected and the clogged area is identified, it's time to start removing the dirt and blocked-up area.

3. Remove The Dirt & Clean The Clogged Exhaust System

The third step is to remove the dirt, grime, grease and any material that should not be in the exhaust manifold or the exhaust system.

Also check the blocks and heads and remove gunk from them too if needed.

Removing the material could be difficult depending on the type of material that is blocking the exhaust system.

Check the risers for clogging and remove the dirt and grime from them too.

Clogged risers can prevent cooling water from entering the exhaust exit piping.

A common place where exhausts get clogged up is in the elbows of the exhaust system.

To remove the dirt and unclog the marine exhaust: 

  • Use a gasket scraper to scrap stubborn dirt: Use a gasket scraper to remove tough dirt that is trapped and clogging up the exhaust
  • Use a whiz wheel tool to help detached hard dirt materials: Use a whiz wheel tool to remove the hardest material blocking the exhaust. Just be careful not to damage the exhaust itself while doing it
  • Use cleaning fluid and a narrow bristle brush: Use a cleaning fluid like Starbrite and scrub away the sludge from the exhaust. Sometimes even carburetor cleaner is not strong enough to remove some of the worst sludge and dirt
  • Use a pressure washer if the dirt is particularly stubborn: If you are having trouble getting the dirt out of the exhaust, try using a pressure washer to blast away the clogged dirt
  • Pour fresh water through the disconnected exhaust system: This is to flush out any remaining dirt or grime and to ensure there is no clogged area left

If none of this works, you will most likely need to replace the exhaust manifold.

Once the exhaust is cleaned and unclogged, you are ready to reattach it.

4. Reattach The Unclogged Exhaust System

The fourth step is to reattach the freshly cleaned and unclogged exhaust system to the boat.

Use the tools to get everything attached properly without any issues. You may find cracked bolts, screws or seals that may need to be replaced at this stage after the exhaust is cleaned.

Replace any damaged parts with new ones and follow the steps in your boat manual for reattached your exhaust system.

Different brands may have slightly different ways of reattaching the exhaust.

5. Start Up The Boat & Check Everything Is Working

The final step is to start up the boat after reattaching the exhaust system and let the motor sit idle for at least 10 minutes.

This is a very important step and should not be ignored. After you reattach everything, you should start the motor and leave it idle to ensure there is nothing broken.

The first restart after unclogging the exhaust system might be extra smoky but this is normal for the first engine start up post unclogging.

If everything is fully functional, the engine should run smoothly without any issues and you are finished.


Following these steps should solve the problems of a blocked exhaust.

If you've unclogged the exhaust correctly, you will notice your engine runs better, there will be less smoke, the fuel consumption will be much better, the engine will not be stuttering, the exhaust manifold alarm will stop and the overall boating experience will be much more enjoyable.