Pontoon Boat Winterization: A Complete Step-by-Step Guide for Protection & Longevity

There’s nothing worse than firing up your pontoon in spring only to discover cracked engine blocks, corroded fittings, or a mouse nest in your upholstery—all preventable with proper winterization.

Why Pontoon Boat Winterization Matters More Than You Think

Pontoon boats aren’t like your average V-hull runabout. Their aluminum tubes, larger deck surfaces, and often exposed storage areas require specific attention when cold weather rolls in. Skip a few steps, and you’re looking at expensive repairs come spring. I learned this the hard way after my first winter as a pontoon owner—a $1,200 lesson I’ll never forget.

Winterization isn’t just about draining water. It’s about protecting your investment from freezing temperatures, moisture damage, corrosion, and critters looking for a cozy winter home. Whether you’re storing your pontoon on a lift, in a garage, or shrink-wrapped at the marina, these steps will keep your boat ready to roll when the weather warms up.

When to Start Winterizing Your Pontoon

Most boaters should begin winterization once water temperatures consistently drop below 60°F or when you know you won’t be using the boat for several weeks. In northern states, that’s typically late October through early November. Southern boaters might wait until December, but don’t push it—one unexpected freeze can cause serious damage.

Understanding What Freezing Water Does to Your Boat

Water expands by about 9% when it freezes. That expansion can crack engine blocks, split water pumps, burst hoses, and damage your livewell system. Even small amounts of trapped water in your bilge, freshwater system, or ballast tanks can cause problems. The goal of winterization is to remove or protect every drop of water in your pontoon’s systems.

Essential Winterization Supplies You’ll Need

Before you start, gather these materials:

• Marine antifreeze (propylene glycol, not automotive ethanol-based—brands like Star brite and RecPro work great)
• Fuel stabilizer (Sta-Bil Marine or Yamaha Fuel Stabilizer + Conditioner)
• Engine fogging oil (CRC or Yamaha Stor-Rite)
• Clean rags and paper towels
• Basic hand tools (wrenches, screwdrivers, pliers)
• Boat cover or shrink wrap kit
• Battery tender or trickle charger
• Moisture absorbers like DampRid

Pro tip: Buy your supplies in September when prices are lower and selection is better.

The Engine: Your Most Critical Winterization Task

Your pontoon’s engine—whether it’s an outboard, sterndrive, or inboard—requires the most attention. Here’s the breakdown:

For Outboard Motors (Mercury, Yamaha, Suzuki):

1. Run the engine with fresh fuel mixed with stabilizer for 10 minutes to circulate it through the system
2. Disconnect the fuel line and let the engine run until it stalls (this empties the carburetor)
3. Fog the engine by spraying fogging oil into the carburetor while the engine runs at around 2000 RPM
4. Change the lower unit gear oil—old oil often contains water that can freeze
5. Remove the propeller and inspect for fishing line around the shaft
6. Grease all fittings on the steering and tilt mechanisms

For Sterndrives (MerCruiser, Volvo Penta):

The process is similar, but you’ll also need to winterize the raw water cooling system. Most owners run marine antifreeze through the system using a pickup hose in a bucket. Follow your manufacturer’s specific instructions—each model varies slightly.

“Skipping the fogging oil step is the number one mistake I see boat owners make. That protective coating inside your cylinders prevents corrosion during storage, and it costs less than $10.” — Marine mechanic with 23 years experience

Protecting Your Fuel System

Stale fuel is a pontoon owner’s enemy. Ethanol-blended gas can separate and cause starting problems or damage fuel components.

1. Fill your fuel tank to 90% capacity (this minimizes condensation)
2. Add the correct amount of fuel stabilizer—most products treat 25 gallons per ounce
3. Run the engine for 10 minutes to distribute the stabilizer throughout the system
4. For long-term storage (4+ months), consider draining the fuel completely

Some pontoon owners prefer to drain their tanks entirely, but I’ve found that filling them with stabilized fuel actually prevents more problems. The key is using a quality marine fuel stabilizer, not the cheap stuff from the gas station.

Winterizing the Freshwater System

If your pontoon has a freshwater sink, shower, or washdown system, you’ll need to flush these lines with marine antifreide.

1. Drain all water from tanks, lines, and the water pump
2. Pour marine antifreeze into the tank or use a pump to push it through the system
3. Open each faucet until you see pink antifreeze coming out
4. Don’t forget the water heater if you have one—drain it completely

Always use propylene glycol marine antifreeze—it’s non-toxic and won’t damage your plumbing. The pink color makes it easy to see when it’s flowing through your system.

Cleaning and Protecting Your Pontoons

Those aluminum tubes need love too. Here’s what I do every fall:

• Scrub the pontoons with a soft brush and boat soap to remove algae and scum
• Check for dents, punctures, or signs of corrosion
• Apply a protective aluminum polish (3M Marine Aluminum Restorer works great)
• Inspect welds and seams for any signs of problems

If you store your pontoon in the water over winter (only recommended in areas without hard freezes), consider using a de-icer to keep water circulating around the pontoons.

Electrical System and Battery Care

Your battery will slowly discharge over winter, and a dead battery can sulfate and lose capacity permanently.

1. Remove the battery from the boat (prevents accidental drain)
2. Clean terminals with a wire brush and baking soda solution
3. Store the battery in a cool, dry place—not on a concrete floor (that’s a myth, but avoid extreme temperatures)
4. Connect a battery tender or trickle charger (NOCO Genius5 is my go-to)
5. Check the charge monthly

For electronics like your fishfinder, chartplotter, or VHF radio, remove any portable units and store them indoors. Fixed electronics should be fine, but I always disconnect them from power to prevent phantom drain.

Comparison Table: Winterization Product Options

Product/Type	Key Features	Benefit	Approx. Cost	Best For
Star brite Marine Antifreeze	Non-toxic propylene glycol, -50°F burst protection	Safe for all plumbing, easy to see	$12-15/gallon	Freshwater systems, all climates
Sta-Bil Marine Formula	Prevents ethanol separation, 12-month protection	Keeps fuel fresh longer	$14/16 oz (treats 80 gal)	Extended storage, ethanol fuel
CRC Engine Fogging Oil	Petroleum-based coating, anti-corrosion	Protects cylinders during storage	$8-10/can	All engine types
NOCO Genius5 Charger	Smart charging, automatic maintenance mode	Prevents battery sulfation	$50-60	Year-round battery health
3M Marine Aluminum Restorer	Removes oxidation, protective coating	Keeps pontoons shiny, prevents corrosion	$18-22/bottle	Aluminum pontoons, trailers

Interior Protection and Upholstery Care

Mold, mildew, and critters are the enemies of your pontoon’s interior during storage.

For upholstery:

• Clean all vinyl surfaces with marine vinyl cleaner
• Apply a UV protectant spray (303 Aerospace Protectant is the gold standard)
• Consider removing cushions for indoor storage if you have space
• If cushions stay on the boat, prop them up for air circulation

For carpeting:

• Vacuum thoroughly to remove dirt and debris
• Shampoo if needed and let dry completely
• Sprinkle baking soda to absorb odors
• Place moisture absorbers in storage compartments

I once made the mistake of storing my pontoon with crumbs and food wrappers on board. Spring revealed a family of mice had moved in and chewed through two seat cushions. Learn from my expensive mistake—clean everything.

Covering Your Pontoon for Winter

A proper cover is your pontoon’s winter coat. You have three main options:

1. Canvas mooring cover ($300-800): Breathable, reusable, good for mild climates
2. Shrink wrap ($200-500 for professional application): Best protection, single-season use
3. Tarp ($50-150): Budget option, requires careful securing and ventilation

I prefer shrink wrap for northern winters because it creates a watertight seal while allowing some moisture to escape through vent patches. If you go with a canvas cover, make sure it has support poles to prevent water pooling and proper ventilation to prevent mold.

Never use a plastic tarp without ventilation—you’ll create a greenhouse effect that promotes mold and mildew.

Trailer Maintenance During Winter Storage

Don’t forget about your trailer—it needs attention too.

• Check tire pressure and inflate to maximum sidewall rating
• Grease wheel bearings (or at minimum check them)
• Inspect lights and wiring for corrosion
• Touch up any rust spots with rust-inhibiting paint
• Place blocks under the frame to take weight off suspension
• Consider jack stands if storing long-term

Here’s something most people don’t think about: mice love to nest in boat trailers during winter. I stuff steel wool in any openings and spray peppermint oil around the frame—mice hate the smell.

Regional Winterization Differences

Your winterization approach depends heavily on your climate:

Northern climates (below freezing for extended periods):

• Complete fuel and water system winterization is mandatory
• Remove battery and electronics
• Shrink wrap or heated storage recommended
• Check your cover monthly for snow load

Moderate climates (occasional freezing):

• Full winterization is still smart insurance
• Canvas covers usually sufficient
• Can leave battery connected with tender
• Monitor weather forecasts closely

Southern climates (rare or no freezing):

• Focus on fuel stabilization and cleaning
• Moisture control is your main concern
• Battery maintenance still important
• Consider partial winterization as insurance

I’m in Minnesota where winter means business, so I don’t take chances. But my cousin in South Carolina does a “light winterization” and keeps his pontoon ready for those random 70-degree January days.

Frequently Asked Questions

How much does professional pontoon winterization cost? Professional winterization typically runs $200-400 depending on your location and boat size. This usually includes engine prep, fuel stabilization, and basic cleaning. DIY winterization costs $50-100 in supplies and takes 3-4 hours for your first time.

Can I store my pontoon outside without a cover? Technically yes, but it’s a terrible idea. UV damage will fade and crack your upholstery within a season, and moisture will corrode electronics and metal components. Even a cheap tarp is better than nothing.

Do I need to winterize if I’m storing my pontoon in a heated garage? You still need to stabilize fuel and protect the engine, but you can skip the antifreeze for plumbing systems. The consistent temperature prevents freezing but doesn’t eliminate other winter storage concerns like stale fuel or battery drain.

What happens if I forget to fog my engine? You might get lucky and have no issues, or you might find corroded cylinder walls that cause hard starting and poor compression. Fogging oil is cheap insurance—it takes five minutes and costs less than $10.

Should I run my pontoon engine during winter storage? No. Starting your engine without running it under load doesn’t get it warm enough to evaporate condensation, which actually causes more corrosion. If you want to run it, take the boat out for a proper ride—otherwise, leave it alone until spring.

How do I know if my pontoons have water in them? Pontoons should be airtight. If you suspect water intrusion, look for these signs: boat sits lower in the water, one side sits lower than the other, or you hear sloshing sounds when moving the boat. This requires professional inspection and repair before winter.

Is marine antifreeze really necessary, or can I use RV antifreeze? Marine and RV antifreeze are usually the same product (propylene glycol), so yes, RV antifreeze works fine. Just make sure it’s rated for your lowest expected temperature and is non-toxic. Never use automotive antifreeze—it’s toxic and can damage rubber components.

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Spring Launch Checklist

When warm weather returns, you’ll want to reverse the winterization process:

1. Remove cover and air out the boat
2. Reinstall battery and check charge
3. Inspect all systems for winter damage
4. Flush marine antifreeze from plumbing
5. Check engine oil and lower unit gear oil
6. Reconnect fuel lines and check for leaks
7. Test all electronics before launching
8. Do a quick test run at the launch ramp

Always check your boat’s specific owner’s manual for manufacturer recommendations—some engines have unique winterization requirements.

Final thought: Winterization might seem like a hassle, but it’s way easier than dealing with spring repairs. I spend about three hours each fall winterizing my 24-foot pontoon, and I’ve never had a single winter-related issue in eight years. That peace of mind is worth every minute.

What’s your winterization routine? Have you learned any tricks that make the process easier? Drop a comment below and share your experience with fellow pontoon owners!