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Yanmar Pleasure Boat Marine Engine Help

I HAVE WATER IN THE ENGINE!

There are several reasons for water in the engine, all the ones I can think of are listed here and if you have any to add, please email me. The fixes below are only general ideas, as usual each problem is different and the specifics will vary. When you do it, do it quickly and don't skimp on the cleaning fluids.

 The boat sank! 

  • If the engine is still in warranty, talk to your insurance broker about replacing it as the warranty will no longer apply.
  • Keep the engine underwater until you have plenty of fresh water, a 20litre (5gal) drum of clean diesel fuel and a large spray can of WD40, CRC 5-56 or equivalent.
  • Haul the boat and immediately wash the engine and engine room down with a fresh water hose. Wash in the air intake and up the exhaust. If the engine is turbocharged don't use too much water pressure on the compressor and turbine wheels.
  • Remove the injectors, flood the cylinders with diesel. Turn the engine over while doing this.
  • Remove all electrical parts, wash them again with the fresh water hose and spray with WD40 or put them into a container of diesel. Take them to the electrical shop for inspection and testing.
  • Remove the complete wiring harness and throw it away. (I don't care what a new one costs, hopefully you've already talked to your insurance broker. It's cheaper than trying to drag your boat off the rocks of a lee shore - in a 50 knot gale - when nothing works some 6 months later)
  • Replace the oil in the sump.
  • If water got into the fuel, drain and clean the tank and lines, replace the fuel.
  • Refit the starter motor.
  • Rotate the engine to pump out the residual diesel. ( Hint: as the diesel in the cylinders will spray everywhere, put a rag or two on top )
  • Refit the injectors, connect a clean fuel source and water supply and start the engine, run it till it's warm. Replace the oil filter, and the oil again if it doesn't look 'squeaky' clean.
  • Reinstall the engine into a refurbished engine room.

Note: If it is immersed in salt water the paint will probably fall off the engine and I don't know any good way of fixing it.

  While trying to start the engine, water came out the air intake! 

  • If the engine is cranked over for a period of time without starting, the exhaust may fill with water as it is normally carried out of the pipe by the exhuast gas. In this case the water may flow back into the engine. It usually happens if you have difficulty while trying to bleed the fuel. Note: The siphon breaker and high rise elbow below will not prevent this happening.
  • If you have trouble bleeding the fuel, turn off the water intake valve (sea cock, Kingston cock) and as soon as the engine starts, turn on the water again.

  Installation problems: 

exhaust gif
  • Referring to the exhaust diagram , we'll start from the left side or stern of the boat. Check that the exhaust outlet is above the water with everyone on the crew (or all your passengers) standing at the stern. If the outlet is under water (or in it), it must be raised!
  • The exhaust does not have to have a gooseneck but it is preferable for inshore and a must for offshore operations. It prevents a following sea from filling the exhaust and engine.
  • The waterlock muffler must be fitted directly in line fore and aft and as close as possible to the mixing elbow.
  • Do not install a waterlock sideways across the boat! As the boat rolls the water gets fired into the engine.
  • Do not install the waterlock the wrong way around. The water coming back down from the gooseneck will projectile vomit itself into the engine!
  • If there is not 250mm / 10 inches between the top of the water in the waterlock and the underside of the mixing elbow, fit the optional high rise exhaust kit shown below. If this height is less than 250mm the water in the exhaust may flow back into the engine while sailing at an angle of heel and/or heavy fore and aft pitching in a short seaway. The high rise elbow adds 50-75mm to the height, depending on the engine model. See the applicable engine brochure for installed height of the engine with this elbow. High rise elbows are optional accessories for GM and JH series. Larger horsepower engines will need a special adapter made for each individual installation.


  • A: Mixing elbow / water injection elbow
  • B: Flexible exhaust hose to the waterlock
  • C: Threaded joint (left and right hand thread)
  • D: Exhaust elbow
  • E: Engine exhaust manifold (raw water cooled engine)
  • F: Cooling water hose
  • G: Underside of Mixing elbow
  • H: Manifold drain


  • waterlock height NOTE: If you have a catamaran and like everyone fishing from the cockpit, make this distance larger or measure it wih your fishermen in place. The bouyancy in the stern is less than a monohull.

  No siphon breaker fitted when necessary: 
Cooling water can continue to siphon into the exhaust after the engine has stopped. When the water pump is new it stops any water flowing past it but as it wears in service water will flow past it. As there is no exhaust gas to carry the water from the exhaust pipe, it will flow back into the engine if the underside of the mixing elbow is at or below the waterline. The small picture above shows the elbow abovethe waterline. (also take into account pitching at anchor or while sailing. ) To prevent this, a siphon breaker ( aka anti siphon valve, vented loop ) must be fitted. If you can't get the height in the engine room, take it into a side locker or up under the coaming.

  Mechanical problems: 

  • There is a blown head gasket
  • Heat exhanger is faulty
  • Cylinder head is faulty
  • Oil cooler is faulty

  • If any of the above occur on a fresh water cooled engine the coolant level in the tank will be down, it may even spray around the engine room from the overflow bottle vent. There may be water in the engine oil.
    Another reason cooling water blows around the engine room is that, on fresh water cooled engines, the overflow bottle connections are reversed on bottles that have more than one connection. Get the tools out and / or call the mechanic.

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