I went through a rather large puddle very enthusiastically in my 2007 Jeep Wrangler the last time there was a hard rain. Well, I think I got some water into the engine when I did that and now the thing is hydro-locked. Very disappointed that a puddle totally wrecked the Jeep motor. What can I do to prevent that from happening again (besides avoiding puddles), after the motor gets replaced?
Have you already determined you damaged the motor?
You may be able to remove the spark plugs and push out all the water, then the air filter can be replaced along with the oil and filter being changed. If the engine still won't turn after the plugs come out, the rods were probably bent and the engine will need to be replaced.
After the above repairs are done, you can install an aftermarket snorkel kit that will raise the intake to the engine and allow you to go in deeper water. Keep in mind that the axles and transmission have vent tubes that can also get water in them. There are aftermarket kits to modify these vents as well. When fording water, just make sure to keep the water below the dash or you will run into a whole lot more trouble.
For the record, I do not condone fording water deeper than what the manufacturer suggests.
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