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Flush The Funk

Is your head, well, stinky? Here are 12 tips that will definitely freshen things up.

Overhead view of a bathroom with white sink and white toilet

Green Cloud: Getty Images

Does your boat stink? If so, in most cases you need look no further than your boat’s head. It was cool to be funky back in the ’70s, but a funky smelling head has no business on today’s boats. Let’s disco down and check out 12 ways to improve the odiferous vibe emanating from your boat’s head.

1. Look For Leaks 

Sanitation system leaks are one of the most common sources of head odors. Start at one end of your sanitation system and work your way to the other, checking each hose joint for leaks while ensuring all hose clamps are tight and corrosion-free. Install double hose clamps where possible, if you have sufficient hose barb to allow it – otherwise you’ll simply be crushing or cutting the hose, causing even more leaks.

2. Check Your System And Hose Runs For Places Where Raw Sewage Can Collect

Hose runs should be kept as short and straight as possible. Holding tank discharge hoses should also be self-draining (e.g., deck pumpout fitting hoses should drain back into the holding tank without loops or low spots).

3. Banish Bilge Funk

One of the more unsanitary practices found aboard boats are showers that drain directly into the bilge. This setup not only generates odors, but also introduces bilge pump-clogging hair and soap scum into the bilge. This can be particularly noticeable in the head area. A common aftermarket solution is to plumb a gravity-fed sump beneath the shower pan, which collects the water and automatically pumps it overboard. If you have a shower sump box, check to make sure it’s working. An inoperative sump will likely be full of water, which can contribute to head odors. Remove the sump cover at least annually to clean the strainer, check the sump pump and automatic float switch for proper operation, and check all electrical connections for corrosion and potential failure.

4. Shock Your Holding Tank

At least once a year (spring or fall), shock your tank to descale the inside and flush the system. Shock treatments help prevent odor buildup and can also be used a second time if odors are noted midseason. It’s also recommended to shock the tank when you haul your boat out for the winter. Add shock treatment a week or so before the last pumpout of the season (while still using the boat), which gives the treatment time to slosh about in the holding tank to help descale the tank for the winter. It also helps ensure a clean last pumpout.

5. Replace Your Hoses 

Sewage can permeate old sanitation hoses, releasing bad smells aplenty. To see if your hose is permeated, wipe a section (particularly a low section where fluids may be collecting) with a warm, damp cloth, drop it in a zipper storage bag, carry it above decks into fresh air, then open the bag and give a sniff. Always use proper sanitation hose when installing or replacing old hoses, including tank vent hoses. Premium rubber sanitation hose has a thicker wall and features two-ply reinforcement and a wire helix. It may sound like overkill, but just remember it has to handle human waste that (on a boat) is roughly 30 times more concentrated than typical residential sewage.

6. Pump Early And Often 

It’s a fact – the more poop you have around, the worse things smell. Pump out your holding tank well before it hits the full mark.

Four images displaying an improperly installed hose, bulge in hose, duck taped hose, head leak

1.Improperly installing a double hose clamp has cut the hose. 2. The bulge in this hose is just begging for a blowout. 3. Even duct tape won’t reduce the smell of a permeated sanitation hose. 4. Smelly head leak Photos: Frank Lanier 

7. Check The Holding Tank Vent Line Regularly For Blockages

Mud-daubers and other such insects love to build nests in them and if the tank is filled to overflowing, bits of sewage can clog the vent line. A clogged vent hose not only promotes smells but can also damage your system due to the buildup of pressure each time the head is flushed. A clogged vent also creates negative pressure when pumping out, which can cause damage and possible collapse of the holding tank. When possible, back flush the vent each time you pump out to ensure it stays open and clear.

8. Rebuild Your Toilet 

Based on the manufacturer’s recommended time frame and before leaks occur, add new gaskets, seals, valves and impellers. The soft parts of your toilet will eventually dry out and become brittle, which leads to cracks and leaks. By replacing these parts on your own terms before they have a chance to fail, you’ll hopefully prevent one of the more common boat owner nightmares – toilet failure (it never happens at a good time) and the emergency repairs necessary to fix it.

9. Flush The Head Sufficiently 

To push all sewage from the hoses and rinse behind it, flush the head. How much extra flushing do you need? Two strokes per every foot of discharge hose is a common rule of thumb. If you’re worried about filling the holding tank too soon, clear the hose once at the end of the day or before leaving the boat after that weekend cruise.

10. Clean Your Head After Each Trip 

Giving sinks, counters, and the areas around and behind the toilet a good cleaning with disinfecting wipes or other such cleaners will leave Neptune’s throne room smelling clean and ready for your next adventure.

11. Consider Converting Your Toilet to a Freshwater Flush Unit

If you boat in saltwater and your toilet uses it as flush water, consider a freshwater flush unit, which will go a long way toward eliminating odors. Converting to freshwater will also prevent calcium buildup (scale deposits) in the discharge hoses, which retains smells and can eventually lead to total blockage of the hose.

12. Flush A Pint Of White Vinegar

If your system uses saltwater, flush a pint of white vinegar through the head monthly to dissolve scale and help prevent future buildup. Flush the vinegar slowly through the system (one stroke of the toilet pump every five minutes or so), and once the vinegar is discharged, flush the system with freshwater. A good follow up to your monthly vinegar treatment is flushing a bit of pump lubricant through the system to keep gaskets and other soft parts supple and in good condition.

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Frank Lanier

Contributing Editor, BoatUS Magazine

Capt. Frank Lanier is a SAMS Accredited Marine Surveyor with more than 40 years of experience in the marine and diving industries. He’s also an author, public speaker, and multiple award-winning journalist whose articles on boat maintenance, repair, and seamanship appear regularly in numerous marine publications worldwide. He can be reached via his YouTube channel “Everything Boats with Capt. Frank Lanier” and website