If enough water is ingested into the engine it can do serious damage, called hydrolocking the engine. (Car Talk has answered a similar question, found here.) Some cars, mainly sports cars, may have a tube or intake passage lower to the ground that is more susceptible to sucking up water. Your average sedan isn’t out of the danger zone, though, and may have an intake tube that sucks in outside air then routes the air back to the air box and filter under the hood. If this air tube is submerged in water or gets a large amount of water splashed into it — possibly by a passing truck — hydolocking can happen.
An engine compresses air and vaporized fuel with its pistons and is not designed to compress water. If water gets into the engine the pistons will try to compress it, and unlike air, water isn’t compressible. Severe breakage is typically the result if enough water is ingested. Our suggestion: Don’t drive through large puddles. Not only can it possibly damage your engine, but hydroplaning into a tree can do a lot more damage to you — people aren’t compressible, either. If faced with a large puddle, simply take it slow and keep an eye on other cars as they drive through the puddle to gauge how deep it is.
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