Are your pontoon tubes covered with stains, algae, scum, and other debris? It looks nasty, reduces your boat’s value, and can even slow your performance down. But did you know that it’s possible to clean pontoon with toilet bowl cleaner safely? In this guide I am going to tell you exactly how to do it, with a method that won’t damage your aluminum.

Here’s the quick steps for cleaning pontoons with toilet bowl cleaner but do scroll down to read each step in more detail so you don’t miss any important parts.

  • Step 1: Rub off any large debris and dirt with a stiff brush
  • Step 2: Clean down the pontoon logs preferably with a pressure washer
  • Step 3: Spray or sponge diluted toilet bowl cleaner onto the pontoons
  • Step 4: Rub the toilet bowl cleaner in and leave for 5 minutes
  • Step 5: Rinse and hose down, then repeat with cleaner where necessary
  • Step 6: Let the aluminum pontoon tubes dry, and then you can move to polishing

! IMPORTANT ! Read the steps in more detail lower down so you know the exact process that won’t lead to you damaging or scratching your aluminum.

How to Clean Your Pontoons with Toilet Bowl Cleaner

When you first bought your boat, remember how shiny those pontoon logs looked?

We’re going to get your pontoons back to looking their best, so take your time to read through all the steps below which take you from the toilet bowl cleaner application, right through to the end where you can polish up for a great finish. 

You will see many of these guides online, telling how you clean up your aluminum pontoon tubes with toilet bowl cleaner. But they will often leave out some key aspects, including the polishing and buffing at the end.

They will also fail to tell you how to clean your tubes properly, so you don’t leave any abrasions or scratches on the aluminum.

This guide is different and is written by someone who actually owns a pontoon boat.

Before you even start, move your pontoon boat away from grass. Toilet bowl cleaner can kill grass, and even seen it eat up a cement drive, so you might want to throw a tarpaulin down if you think you are going to be making a mess.

Let’s get started. 

1: Rub Off Any Large Growth with a Stiff Brush

You might end up skipping this step, depending on how long your boat has been in the water, and the degree of growth that’s present.

I’ve seen pontoons that have been left in the lake for years, and when you see under those pontoons it’s insane the amount of growth on there.

The quickest way to get started in cases such as this is to use a stiff brush (not wire or metal brushes!) on a long handle and work to knock off the big stuff.

2: Prepare & Clean Down the Pontoon Tubes

You can also skip this step if you just have some minor stains on your aluminum tubes, but if you’re dealing with a lot of scum, algae, and heavy debris, then before you even consider using toilet bowl cleaner, you need to attack the larger dirt.

The best way to do that is to use a pressure washer.

It will hammer away at the really tough stuff, and help you to blast it off, as toilet bowl cleaner definitely won’t let you do that.

I have a Sun Joe pressure washer which has served me really well since I owned my Bennington. I also use it for cleaning up my vinyl flooring, so it’s well worth the money you pay for it. It’s cheaper than a Karcher pressure washer but works just as well.

Simply spray in an and up down motion until the bulk of the scum has gone.

Your pontoons are still going to be dirty, but that’s where cleaning with toilet bowl cleaner is going to come in with the next couple of steps.

3: Spray or Sponge Diluted Toilet Bowl Cleaner on the Pontoons

Firstly, is toilet bowl cleaner safe to use on pontoon aluminum?

Yes, it is, but you need to dilute it properly and take a lot of care when applying it so not to leave abrasions on the aluminum, as that could attract even more algae growth and debris in the future.

Cleaning pontoon tubes with toilet bowl cleaner is cheaper than acid solutions you might be advised to buy, and actually just works as well.

But you need to do it right.

Cleaning a Pontoon with “The Works”

The best toilet bowl cleaner for cleaning pontoon boats is a product called The Works (view it on Amazon). I have had zero problems with this product, and no abrasions were left on the aluminum when using this cleaner.

To apply it, you have two options.

The best way is to use one of those cheap one-gallon sprayers, it will make your job easier and quicker and let you apply the cleaner evenly across the pontoon tubes.

Again, there’s a sprayer on Amazon that I recommend and use myself with my cleaning set-up.

Don’t just spray toilet cleaner on in its undiluted format. You will need to mix it up at a 1-part cleaner to 2-parts warm water ratio.

Once you have your mix ready to go, spray in up and downwards motions until you get an even coating.

Just work on one patch or panel at a time. The reason I do this is because if the toilet bowl cleaner dries on, you’ve just made your cleaning job that much harder.

By working on one patch at a time, you will get better results. I tend to work in 3-square foot patches, or up to an aluminum welding join. Whatever works best for you and the time you have.

Alternatively, if you don’t want to buy a sprayer, you just mix it all up in a bucket and use a sponge to apply the toilet cleaner mix onto the tubes.

4: Rub the Toilet Bowl Cleaner In, Leave for 5 Minutes

Once you have a coat of toilet bowl cleaner on the aluminum pontoon patch, use a sponge and start to rub in with circular motions. No need to push too hard, and whatever you do, don’t use a abrasive scouring pad for this, it will scratch up the metal.

Now it will look like you’re rubbing and pushing dirt around the aluminum patch you are working on, but don’t worry as in the next steps we’re going to do hose down.

5: Rinse & Hose Down, Repeating if Necessary

You don’t want the toilet bowl cleaner to completely dry, as you will then have to try and clean that off as well, so a 5-minute wait is just about right.

After the 5 minutes is up, you can hose down the patch using a standard garden hose connected up to an external house tap.

Once you have hosed the patch down with clean water, take a look at the results and make the decision on whether you need to go again.

On most occasions, just one application and clean will do, but for more stubborn stains on pontoons that have been left in water for a long time, you might need to go again.

If you are happy with the look after the hose down, for an even better clean, I then use a wet cloth with some clean water for another rub.

6: Let the Aluminum Pontoon Tubes Dry Then Polish

Let the cleaned aluminum dry completely. You can let it air dry or use a dry towel instead as this can help to prevent water spots.

This next polishing step is optional.

Chances are that your pontoons are going to look dull, so for a really clean and shiny finish you can polish and buff them up.

I go into the polishing process in a lot more detail in this guide to polishing pontoons, but in simple steps it goes like this:

Using a variable speed polisher, work in circular motions over the aluminum pontoons, then polishing with little S-shaped movements to blend in any lines.

This isn’t an easy job, and you might be expecting to be doing this for a couple of hours if working on a 22-foot pontoon boat.

You will ache afterwards!

polishing the tubes after you have used toilet bowl cleaner

It’s hard work, but you can get great results (image shared on Facebook, credit unknown).

Once that’s done, you can mix 1-part Shark Hide sealant and protectant to 3 parts water.

This stuff is great for adding a layer of protection onto pontoons and will mean you won’t get as much dirt and debris attached to them in the future.

You can read the instructions that come with Shark Hide, as it’s specifically designed for this type of job.


And that’s it.

I hope that you have find this guide on how to clean your pontoon with toilet bowl cleaner helpful.

If you can, I would appreciate it you pay it forward, and use the social sharing icons on this page to get more awareness out there.