How to Winterize a Marine Sanitation System: Step-by-Step Guide

By Brian Gordon, Last updated: 6/23/2026

Why Winterize?

In the event of a hard freeze, residual water in your boat’s sanitation system could turn into ice and cause expensive damage to your marine toilet, toilet pumps and holding tank. Protecting marine sanitation systems against freeze damage is actually quite easy and we’ll walk you through how to get the job done.

The damage a freeze causes to a marine sanitation system is not always obvious until spring. Water trapped in a toilet pump, joker valve housing, macerator or hose fitting expands when it freezes and cracks plastic housings, splits hoses and destroys pump diaphragms. These are not inexpensive repairs — a cracked macerator pump or split holding tank fitting can easily cost several hundred dollars in parts and labor, plus the misery of discovering the failure on the first warm weekend of the season. Spending 30 minutes and a few dollars on marine antifreeze in the fall is the obvious alternative.

How to Winterize Your Marine Sanitation System

The goal of sanitation system winterization is straightforward: replace every pocket of standing water in the system with antifreeze so there is nothing to freeze and expand. Water hides in toilet pump housings, joker valves, hose loops, y-valve bodies, strainers and the holding tank itself. A complete job touches every one of these points.

What You’ll Need

• Non-toxic propylene glycol marine antifreeze — at least one gallon for a typical installation; have two on hand for boats with multiple heads or long hose runs
• A small bucket or container to hold the antifreeze while the intake hose draws it in
• Screwdriver and hose clamps for reattaching the raw water intake hose
• Rags or paper towels for cleanup
• Gloves — propylene glycol is non-toxic but messy

Step One: Pump Out and Flush the Holding Tank

To winterize your sanitation system, start by making sure the holding tank is pumped out. To start “with a clean slate” in the spring, now is the time to give it a thorough flushing with fresh water.

Do not skip this step. Winterizing a holding tank that still contains waste locks that waste in the tank over the entire storage period, allowing odors to penetrate hoses and tank walls and creating a genuinely unpleasant spring recommissioning job. Pump out at a marina pump-out station, flush the tank with fresh water through the toilet until the discharge runs clear, pump out again, and then proceed with antifreeze. Your nose — and your spring self — will thank you.

If your holding tank has an inspection port, this is also a good time to open it, check for any cracks or fittings that look corroded, and verify the vent line is clear. A blocked vent line causes pressure buildup in the tank and is a common source of slow sanitation odors that are often misdiagnosed.

Step Two: Disconnect the Raw Water Intake Hose

Remove the raw water intake hose from the seacock and place it in a small bucket with antifreeze.

The raw water intake hose is the hose that runs from the through-hull seacock to the toilet’s pump inlet. It is typically a 5/8” or 3/4” reinforced hose secured with a hose clamp at the seacock fitting. Before disconnecting it, close the seacock completely — this is the valve mounted at the through-hull. Closing the seacock first prevents seawater from flooding your bilge when you pull the hose. Once the clamp is loose and the hose is disconnected, place the open end into your bucket of propylene glycol antifreeze. The toilet’s pump will draw the antifreeze through the system in Step Three.

Use roughly a quart of antifreeze in the bucket to start — enough for the pump to draw without running dry. Have a second quart ready. You want antifreeze visible in the toilet bowl and running through to the holding tank before you stop, which confirms the entire intake side of the system is protected.

Step Three: Flush the Head to Circulate Antifreeze

Flush the head to circulate the antifreeze through the lines and to the holding tank. Then, double clamp the hose back on to the seacock.

Operate the toilet pump — either by flushing or manually pumping, depending on your toilet type — until you see pink antifreeze coming through the bowl and the water in the bowl is clearly antifreeze rather than water. This confirms antifreeze has passed through the intake pump, the pump housing, the joker valve and the discharge line. Continue pumping several more strokes after you see pink at the bowl to push antifreeze further down the discharge line toward the holding tank.

If your toilet has a electric flush, run it in short bursts to avoid burning out the pump motor while it draws from a small bucket. Manual pump toilets can be pumped continuously without issue.

Once antifreeze has circulated through the system, reconnect the raw water intake hose to the seacock and secure it with two hose clamps — staggered so the ears of each clamp are on opposite sides of the hose. Double clamping is a best practice on all below-waterline hose connections: a single clamp failure at a raw water intake can sink a boat. This is a good moment to inspect the hose itself for cracking, brittleness or soft spots. If the hose is more than five years old or shows any deterioration, replace it before reassembly.

Step Four: Purge and Fill the Raw Water Strainer

Make sure the raw water strainer is purged and filled with antifreeze as well.

The raw water strainer — a clear plastic canister with a mesh basket inside, typically mounted in the intake line between the seacock and the toilet pump — traps debris before it reaches the pump. It retains standing water after each use and is one of the most commonly overlooked winterization points. A cracked strainer body is an extremely common spring surprise for boats that skipped this step.

To winterize the strainer: with the seacock closed, open the strainer cap (usually a large plastic ring that threads on), remove and rinse the mesh basket, then pour antifreeze directly into the strainer body until it is full. Replace the basket and cap, ensuring the cap o-ring is seated correctly. If the o-ring is flattened, cracked or shows any deterioration, replace it now — a leaking strainer cap at the seacock is a bilge water problem waiting to happen in the spring.

NOTE: If you have a waste treatment device such as Raritan’s Electro Scan, it too must be winterized. Improper winter lay up of these devices is a major cause of failure due to freezing of residual water. Follow the manufacturer’s instructions. For complete instructions on Electro Scan winterization, refer to the Electroscan manual.

About Antifreeze

West Marine non-toxic propylene glycol antifreeze is recommended for winterizing potable water, sanitation, air conditioning systems and engines.

There are two types of antifreeze. The first is common automotive antifreeze, such as Prestone, which is ethylene glycol. This type of antifreeze is highly toxic and should not be used for winterizing applications on boats. In place of ethylene glycol, use non-toxic propylene glycol, like West Marine Brand Engine and Water System Antifreeze. For northern regions where the temperature can drop below zero, we recommend antifreeze with a freeze rating of at least -100°F. Why use -100°F antifreeze when the temperature never goes below -50°F? The answer is that what goes into the system as -100°F antifreeze does not come out as -100°F antifreeze. There is always some residual water that lowers the concentration of antifreeze, so the resulting freeze point may be much higher than the rated temperature. The small cost difference between the -50°F, -60°F and -100°F antifreeze is a bargain for the peace of mind you get knowing that your systems will be safe, no matter what the weather. To learn more about antifreeze formulations, check out Antifreeze 101.

One practical note on antifreeze color: most propylene glycol marine antifreeze is pink or red, which makes it easy to confirm visually that antifreeze has reached each point in the system. When you see pink at the toilet bowl after flushing, when the strainer body fills pink, and when the raw water strainer basket is submerged in pink fluid, you can be confident the system is protected. Clear or lightly tinted antifreeze works equally well chemically but makes this visual verification harder.

Common Winterizing Mistakes to Avoid

• Skipping the y-valve. If your sanitation system has a y-valve that routes discharge either overboard or to the holding tank, that valve body contains standing water too. After circulating antifreeze through the system, operate the y-valve through its full range of motion so antifreeze contacts the valve seat and seals on both sides. Leave it in the “to holding tank” position for winter storage.
• Not pumping enough antifreeze. Flushing once is often not enough to push antifreeze through the full length of discharge hose to the holding tank. Pump until you see antifreeze color in the bowl, then continue pumping a dozen more strokes. Long hose runs on larger boats may require pumping an entire quart through the system after the bowl first shows color.
• Forgetting the joker valve. The joker valve is a rubber duckbill check valve in the toilet pump that prevents backflow. It sits in a small housing that holds water. If your toilet has been sluggish or slow to flush, the joker valve may already be deteriorating. Winterization is a good time to inspect and replace it — a failed joker valve in spring means odors and backflow into the toilet bowl.
• Using automotive antifreeze. Ethylene glycol automotive antifreeze is toxic to humans, animals and marine life. It should never be used in any boat system that contacts drinking water, and it should not be discharged into the water. Use propylene glycol specifically rated for marine sanitation use.
• Not labeling the seacock as closed. After completing winterization, the raw water seacock for the head remains closed. Tape a note to the seacock or helm console reminding you — or whoever commissions the boat in spring — to open it before operating the toilet. Running a marine toilet with the seacock closed burns out the pump in minutes.

Spring Recommissioning

Recommissioning the sanitation system in spring is essentially the reverse of winterization, with a few additional checks.

• Open the raw water seacock fully before operating the toilet for the first time.
• Flush the system several times with fresh water to clear residual antifreeze from the lines, pump and bowl. Propylene glycol is non-toxic and will not harm the system, but flushing it out before regular use is good practice.
• Check the raw water strainer o-ring and basket — confirm the cap is tight and there are no leaks before leaving the dock.
• Inspect all visible hose connections for any soft spots, cracking or weeping that may have developed over winter. Hoses that were marginal in the fall are prime candidates for failure in spring.
• Test the y-valve operation if your system has one. Valves that have sat in one position all winter sometimes stiffen or seize. Work the valve back and forth several times before the first underway trip.
• If you smell anything from the sanitation system after the first few flushes, check the vent line and joker valve before assuming a bigger problem. These are the two most common sources of spring odor issues after a properly winterized layup.

Best Practice for Antifreeze Disposal

Even though Pure Oceans propylene glycol antifreeze is non-toxic, best practice dictates that you not discharge it on to land, into storm drains or directly into the water. After use, dispose of used antifreeze in a manner consistent with federal, state and local regulations.

Many marinas collect used antifreeze during the winterization season — check with your marina office before disposing of it elsewhere. Propylene glycol is biodegradable but can still deplete oxygen in water if discharged in large quantities, which is why responsible disposal matters even for non-toxic formulations.