If you are confronted with water in an engine, the first place to look before disassembling the engine and checking for a porous block, cracked head, eroded exhaust-water passage, frozen oil cooler, or other labor-intensive issues, is the Yamaha thermostat. Remember that some engines have two thermostats, like Yamaha's V-engines.
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To locate the Yamaha thermostat(s), be sure to refer to the service manual as the location varies by engine. The service manual procedure states that you should put the thermostat in a pot of hot water and check if it opens and closes at the correct temperature. If you do not have access to this method, then an infrared temperature gun can be used at the thermostat housing to get an indication of engine temperature. Again, refer to the service manual for the correct temperature operating range.
If you’ve determined that the engine is running cold, it’s a good indicator that the thermostat is stuck open. Remove the thermostat housing and inspect it. If it is stuck open, replace the thermostat with a new one and be sure to do several oil and filter changes to ensure water is removed from the engine’s oil.
You might be wondering how water gets into the oil due to a thermostat being stuck open. If the engine is running cold, the hot oil meeting a cold engine can produce condensation. The condensation eventually condenses into water and falls into the oil. With an engine running cold, water isn’t the only pollutant getting into the oil. The piston rings (running cold) won’t fully expand to thoroughly seal against the cylinder wall, and may allow a small percentage of raw fuel to constantly seep past them and collect in the sump. Prolonged running with this condition can cause the oil to develop a milky residue. Debris can also get stuck in thermostats and prevent them from retracting back to the closed position.
If you suspect water in the engine oil, there are a couple of quick ways to check. One way is to remove and look at the underside of the oil cap to see if there’s moisture in it. Another way is to pull out the dipstick to check for moisture in the oil. Either method is effective. Yamaha thermostat issues can be prevented by flushing the engine regularly per the owner’s manual.