How to Clean a Pontoon Boat

If you’re the proud owner of a new Avalon pontoon boat, you surely want your craft to last as long as possible.

Besides careful handling and mechanical maintenance, regular cleaning will keep your vessel looking and performing its best for many years.

General Principles for How to Clean a Pontoon Boat

In order to properly clean your pontoon boat, there are several general principles you should make sure you follow, for both the effectiveness of the clean as well as protection from any potential risks that come with improper cleaning.

Which Cleaning Products Should I Use?

For general regular cleaning, the best cleaning products are light and mild. Soft rags or paper towels are best to avoid any affectation of the surfaces, along with mild all-purpose cleaning fluid for most scenarios.

For any carpeting, a vacuum should be all you need for the daily cleanings, saving the more advanced carpet-cleaning products for end-of-season cleaning.

How Often to Clean

Give your craft a light rinse-down after every outing and more thorough cleaning at the start and end of the season.

While wooden flooring and metal components may not require cleaning after every outing, it is best practice to vacuum any carpets and wipe down any furniture. Anything that has a tendency to gather dirt should be cleaned at a heightened regularity.

Cleaning Aluminum Boats

Giving the boat’s aluminum components (the pontoons and the side panels) a thorough waxing every three to six months helps keep it in the best condition during summer.

In luxury models, aluminum is restricted to the pontoons, while the exterior uses fiberglass. This fiberglass will also benefit from a thorough waxing each season.

What to Avoid

Avoid using chemicals such as acetone, thinners, or gasoline to remove encrustations of bird droppings or other substances clinging to your vessel: they will strip the paint. Also, avoid using pressure washing equipment, which is potentially damaging.

How to Clean a Pontoon Boat for Winterizing

Unless you live in a part of the country with year-round good weather, your pontoon boat will spend a good portion of the year in storage over winter. Cleaning is imperative before winterizing your boat.


Leaving grime and algae to dry out and harden on your vessel over winter makes them challenging to remove come summer. Do not leave barnacles or zebra mussels to get locked onto your hull. Cover your boat over winter.

How to De-Winterize a Pontoon Boat

When your pontoon boat comes out of storage at the start of summer, de-winterize it with a good cleaning.

Check for any rodents or other pests that may have snuck in, and identify any patches of mildew or mold for special attention. These will require cleaning solutions formulated for removing fungal growth.

Use liquid soap and water to clean all fiberglass components. Use purpose-formulated aluminum cleaning solution for aluminum parts – avoid household cleaners that often contain compounds that will react with aluminum and damage it.

How to Clean a Pontoon Boat Used for Fishing

Pontoon boats are great for fishing. But fishing brings its mess: bait, blood, fish slime, mud, and bits of aquatic weed. Ensure you remove this gunk and wash any residue immediately after getting home—also, always clean fish boxes, coolers, and baitwells.

Cleaning the Flooring of a Pontoon Vessel

Cleaning Marine Vinyl

Brush off the loose dirt, and hose off what is still clinging. Make up a warm liquid soap solution, and gently brush the vinyl. Hose away all the soap residue, and leave the vinyl to air dry.

Should any substance spill on woven vinyl, take action as soon as possible to prevent staining. Follow the steps above, but use oxygen bleach (hydrogen peroxide) in the cleaning solution.
Image of seating area on Tahoe Cascade Quad Lounge

Cleaning Wooden Decks and Flooring

If you opt for a wooden deck, look after it. Ironically, over-cleaning is more likely to wreck a deck than neglect.

As with other components of a pontoon boat, the wood of your deck is vulnerable to corrosive substances. Avoid using caustic substances and chlorine bleach to remove grime—oxygen bleach is okay.

Using a gentle cleanser, such as ECO-100 or ECO-300, scrub across the wood’s grain with a soft bristle brush or pad. Rinse off the residue with water.

Under no circumstances scrub *with* the grain; this will lift out the softer wood in the boards, creating a rough, ridged surface that accumulates grime and water, allowing mold and mildew to thrive and shortening the wood’s lifespan.

While we do not recommend pressure washing any part of your craft, this goes double for using them on a wooden deck. The force blasting away the softer pieces of the wood will achieve in one fell swoop what you could only achieve over many months by hand-scrubbing with the grain.


Marine carpeting is easy to clean. Vacuum up loose dirt frequently, including before washing. Use a standard carpet cleaner to wash it, following the manufacturer’s instructions. Spot clean marks, ensuring that you remove soap residue afterward. Failure to remove it correctly results in particles being drawn to the area, causing the stain to reappear.

Cleaning Seats on Pontoon Boats

Use a warm soap solution or a specialty mold and mildew product, spraying it over the seats and upholstery. Wipe the excess away with an absorbent cloth. Avoid scrubbing vigorously or using a brush, which can harm the fabric’s surface. Entertainer craft are particularly prone to spills of substances that may stain the upholstery or carpeting; dealing with these promptly is the best course.

How to Clean a Pontoon Boat: The Damaging Effects of Saltwater

Saltwater has a powerful corrosive effect on metals, including aluminum, especially when stray electric current from onboard equipment interacts with the salt ions.

The sea also hosts some impressive (and scary) bacteria that can digest substances such as metal and concrete. Other organisms, such as mussels and barnacles, may grow on your vessel’s pontoons, fouling them.

To prevent such effects, apply anti-fouling paint where appropriate, and consider using zinc anodes. Regularly inspect the paintwork and electrical connections, and repair any damage.

Avalon homepage, with a Catalina cruising in the open water.

How to Clean a Pontoon Boat After Saltwater Exposure

Wash your entire boat with fresh water when you use it in saltwater. Let it dry, then cover it to protect it against the elements and air-borne salt particles. Do not cover it wet; the high humidity in coastal areas will result in mildew developing. Flush any seawater accumulated between trailer bunks and the boat’s pontoons, and regularly check the underside of your craft for salt buildup. Flush the engine after every use in saltwater.

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