How to Clean Pontoons on Pontoon Boat: Oxidation, Polishing, and More

Like it or not, bare aluminum is always subject to surface oxidation. Add to that the algae and mineral buildup, and you’ll be amazed by the amount of dullness and discoloration that can happen to your pontoons.

Luckily, dirty pontoons aren’t less durable than clean ones. However, your luxury furniture and railings will look their best over shiny pontoons.

In this guide, I’ll show you how to clean pontoons on a pontoon boat. The process is fairly easy; it won’t take more than 3 hours max. Without any further ado, let’s “dive” right in!

By the way, as an Amazon Associate, I earn when buying qualified products through links on my site.

How to Clean Pontoons

Step 1: Give It a Quick Wash

As you may already know, the aluminum oxidation and buildup will need a specialized cleaning solution. But before that, I always recommend starting with a quick spray with a pressure washer. This should remove any algae or soft buildup, which would increase the efficacy of the cleaner.

If you don’t have access to a pressure washer, use a wet rag with a spray bottle.

Boaters who dock their pontoons for days at a marina will probably need to invest more time and effort in this step. If you trailer your boat after each use, the amount of buildup will be minimal.

Step 2: Pick a Cleaner 

Luckily, there are dozens of different cleaners on the market for you to choose from. (these items are from Amazon)

I don’t want to be decisive, but I think Bio-Kleen’s Aluma-Kleen and Sharkhide’s Aluminum Cleaner are the best. The latter is a bit more expensive, but it’s also more concentrated. I’d highly recommend it if you haven’t cleaned your pontoons for years.

Some boaters prefer to stay on the affordable extreme by using a toilet bowl cleaner. However, this will likely work your fingers to the bone!

Step 3: Wear Safety Equipment

Since most cleaners are based on corrosive acids, you’ll need to wear the following safety equipment before starting. (these items are from Amazon)

  1. Sleeved rubber gloves: to safely brush the cleaner while protecting your clothes
  2. Vapor respirator: to protect your lungs from the acid mist
  3. Eye goggles: to block accidental acid splashes
  4. Long sleeves and pants: to shield your skin from acid burns

If the acidic solution comes in contact with your bare skin or hair, stop working at once. Flush with fresh water for at least 15 minutes to make sure no acid remains over your body.

If your eyes were splashed, hold your face under running water for 15-20 minutes while letting the stream flood your eye. It’s also advised to retract your lower eyelid with your finger.

Whether you have symptoms or not, it’s a good idea to consult a doctor after acid injuries. You may have to use special drops and ointments to prevent long-term damage.

Step 4: Apply the Cleaner 

Whatever cleaner you choose, the process is similar. You’ll need to apply the cleaner, scrub it with a brush and let it sit for a while before rinsing it off. (these items are from Amazon)

If you can spare some cash, investing in a 1-gallon pump sprayer would be ideal if you want to clean a whole pontoon in one pass. If you’ll work with a rag, divide each pontoon into small sections. Asking a friend for help should make the job much more fun and manageable.

For optimal safety, I recommend getting a brush with an extending handle. This should keep acid splashes at bay.

After brushing, leave the acid in contact with the aluminum surface for 5 to 10 minutes. It’s important to never let it dry. If it dries, it’ll harden up and form new deposits that are much harder to clean. To be safe, check the suggested setting time on the cleaner package.

For extra grimy pontoons, applying a single acid coat probably won’t cut it. Contrary to common belief, leaving the cleaner on for additional minutes won’t make any difference. Instead, rinse the old cleaner and repeat the steps.

Step 5: Polishing (Optional)

By now, your pontoons should be free of discoloration, buildup, and algae. For some boaters, this may be more than enough. But if you want your pontoons to shine like mirrors, polishing would be the answer. (these items are from Amazon)

First of all, you’ll need to get a polisher. Choose whatever brand you like, but make sure there’s a speed dial that can fine-tune the speed according to your preferences.

For the polish solution, I haven’t seen anything more effective than Sharkhide Metal Polish and Bio-Kleen S07401 Metal Polish.

How to Apply

  • Start by painting the polishing solution over a small section of the pontoon. Then, grab the polisher with a polishing pad installed and start working the solution around.
  • Never work in random up/down strokes, though. This will likely leave some ugly swirl patterns. Instead, move the polisher in wide “S” patterns.
  • If you’re not happy with how shiny the pontoons look, don’t be afraid to apply additional coats.
  • After you finish, wipe the pontoons with a microfiber cloth to pick up any polishing residues. As you might imagine, these residues can harden up with time and form new deposits. You can also use the polisher with a clean polishing pad to effortlessly absorb these residues.
  • The polishing process will probably take about 2 to 4 hours to finish. You can save your time and effort by skipping the areas lying below the waterline.

Step 6: Clean It Again (Optional)

If you want that mirror-like polish to last for the longest time, do a final pass with the aluminum cleaner. To avoid being redundant, you can just refer back to step 4.

Before you proceed, you’ll need to wipe your pontoons with a clean microfiber cloth. Make sure there is no remaining acid, polish, or even water.

Step 7: Use a Polish Protectant

If you take your shiny pontoons into the water immediately after cleaning, your hard work won’t pay off. They will revert back to that awful black color in no time. Why? Because you’ll be leaving the aluminum bare for air oxidation and mineral buildup. (these items are from Amazon)

Solution? Use a polish protectant. Without getting into technical details, this substance binds to the aluminum surface on a molecular level. This reduces the reactivity by blocking the air and minerals from reaching the aluminum particles.

For that matter, most boaters use Sharkhide Metal Protectant. It’s ideal because it protects your pontoons regardless of your locale. Be it fresh, brackish, or saltwater, Sharkhide works like a charm!

And just like other Sharkhide products, it lies a bit on the expensive side. Then again, this is better than opting for a cheap protectant that turns yellow after a couple of months.

How to Apply

  • Unlike the previous steps, the metal protectant needs to be applied in a specific method to guarantee maximum effectiveness.
  • To start, get a 100% cotton cloth and soak it with the liquid. I prefer cotton to benefit from its impeccable absorbency.
  • Start swiping each pontoon in one pass lengthwise. Don’t go in circles, just one swipe from the bow to the stern. Then scoot down and return with another full wipe. Do this until you cover the whole area.


Knowing how to clean pontoons on a pontoon boat might not have a role in the durability of the pontoons, however, it’s a must if you want to amaze everyone who glimpses your boat.

As an additional tip, it’d be ideal if you can quickly spray your pontoons with water after use, especially if you drive in brackish or saltwater.

Now go on. The boat won’t scrub itself!


Peter is a software developer who loves to take every opportunity to go outside that he can get. Peter grew up going on long backpacking excursions with his family every Summer and now enjoys staying at the beautiful Texas State Parks and swimming in the amazing Texas Rivers.

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