Flush your engine with fresh water using flush muffs or a similar device attached to the raw water pickup. Let all water drain from the engine. Wash the engine down with soap and water and rinse thoroughly. Disconnect the fuel hose and run the engine until it stops. It is important to follow a step-by-step process to make sure that all fuel is drained from the carburetor to prevent build-up of deposits from evaporated fuel. Use fogging oil in the cylinders to lubricate the cylinder walls and pistons. Apply water resistant grease to the propeller shaft and threads. Change the gear oil in the lower unit. Lightly lubricate the exterior of the engine or polish with a good wax.
Run the engine to warm it up and change the oil while it is warm. This allows impurities to be drained away with the oil. Change the oil filter(s). Flush the engine with fresh water. Circulate antifreeze through the manifold by using a pickup hose from the waterpump to a bucket of antifreeze. Start the engine and allow the antifreeze to circulate until water starts to exit the exhaust. This process will vary slightly depending on whether you have a "Raw Water" cooling system or an "Enclosed Fresh Water" cooling system. While you're in the engine room, change the fluid in your transmission. Remove spark plugs and use "fogging oil" to spray into each cylinder. Wipe down the engine with a shop towel sprayed with a little fogging oil or WD-40.
Thoroughly inspect the stern drive and remove any plant life or barnacles from the lower unit. Drain the gear case and check for excessive moisture in the oil, which could indicate leaking seals and the need for repairs. Clean the lower unit with soap and water. If your stern drive has a rubber boot, check it for cracks or pinholes. Grease all fittings and check fluid levels in the hydraulic steering or lift pumps. Check your owner's manual for additional recommendations by the manufacturer.
Fill your fuel tank(s) to avoid a build up of condensation over the winter months. Add a fuel stabilizer by following the instructions on the product. Change the fuel filter(s) and water separator(s).
Make sure the bilges are clean and dry. Use soap, hot water and a stiff brush to clean up any oil spills. Once the bilges are clean, spray with a moisture displacing lubricant and add a little antifreeze to prevent any water from freezing.
Fresh Water System
Completely drain the fresh water tank and hot water heater. Isolate the hot water heater by disconnecting the in and out lines and connecting them together. Pump a non-toxic antifreeze into the system and turn on all the faucets, including the shower and any wash-down areas until you see the antifreeze coming out. Put non-toxic antifreeze in the water heater.
Pump out the holding tank at an approved facility. While pumping, add fresh water to the bowl and flush several times. Use Vanish crystals or whatever your owner's manual recommends that will not harm your system and let it sit for a few minutes. Add fresh water and pump out again. Add antifreeze and pump through hoses, holding tank, y-valve, macerator and discharge hose. Check your owner's manual to make sure that an alcohol-based antifreeze won't damage your system.
Once you have taken care of the systems, should remove any valuables, electronics, lines, PFD, fire extinguishers, flares, fenders, etc. Over the winter, clean, check and replace these items as necessary. Open all drawers and lockers and clean thoroughly. Turn cushions up on edge so that air is able to circulate around them or, better yet, bring them home to a climate controlled area. Open and clean the refrigerator and freezer. To keep your boat dry and mildew-free you might want to install a dehumidifier or use a commercially available odor and moisture absorber product.
Pressure wash the hull, clean barnacles off props and shafts, rudders, struts and trim tabs. Clean all thru-hulls and strainers. Open the seacocks to allow any water to drain. Check the hull for blisters; if you find any that require attention, consider opening them to drain over the winter.
Close all seacocks and check rudder shafts and stuffing boxes for leaks, then tighten or repack as necessary. Check your battery to make sure it is fully charged, clean the terminals, add water if necessary and make sure your charging system is working. Check the bilge pumps to ensure they are working, that the float switches properly activate the pumps, and that they are not hindered by debris. Make sure to check your boat periodically or have the marina check it and report to you. If the water in which you are docked or moored tends to freeze, you should install a de-icing device or bubbling system around your boat.
Like boats, trailers need some attention in the fall so they'll still be rolling in the spring. Hubs that have been immersed in water during the season must be cleaned thoroughly. Rusted areas on the frame should be sanded, primed, and repainted. Tires should be inspected, especially the sidewalls, which tend to crack and wear out before the treads. Finally, removing the wheels and adding support at the blocks under the frame rails will prolong the life of the tires, minimize sagging on the springs, and discourage theft.
You may want to leave a battery aboard your boat to operate a burglar alarm or an automatic bilge pump. These are both useful in the winter, but don't expect an automatic pump to overcome bad deck, cabin, or hull leaks—not in the summer or winter. The pump, battery, or float switch can fail, leaving the boat unprotected. A boat with chronic leaking problems should be dry-stored and repaired as soon as possible.
If you do leave a battery aboard, make sure the cells are filled with distilled water and fully charged so they don't freeze. Frozen cells will ruin a battery. Clean the terminals with baking soda, and rinse with cold water. Coat the terminals and cables with petroleum jelly to help prevent rust. If you don’t need a battery aboard, take it home and do all of the above anyway. Store batteries in a cool dry room and put them on a trickle charger or charge them every 30 to 60 days.
Invest in a cover to keep your boat clean and free from dirt, water, falling leaves and bird droppings, all of which can cause damage if left unchecked. A cover can also prevent UV rays from breaking down hoses and fading carpets and upholstery. During the winter a frame should be used under the cover to distribute the weight of water or snow that may collect on the boat.