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Driving down the highway in a rain storm then i hear this loud popping! Must have been some water came in the grill and hit the heat shield?

 
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damn that happens to me all the time too especially when its raining outside, i went to honda and told them to fix it , and they made up some bs saying that they replaced the manifold sheild , i later found out they lied,. So i toook it back and they said its probably ur aftermarket muffler< i wasnt in the mood to argue that day so im going to take it back again !

 
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if you have exhaust it might be that, other times it could be the wheel well. But if you have an exhuast it is more than likely that. Does it sound like it is coming from under the car?

 
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and don't argue with them because exhausts will do that. It is because your exhuast piping will be hot and then having water hit it will make the piping contract and it changes the sound and makes it vibrate. It can also do that if somehow water gets into your muffler.