Hitting a puddle doesn't do a thing... a flash flood pond and you're screwed... BUT There are intermediate relief inlets you can add to prevent such suction from pulling in any significant quantity of water; the most common is a cylindrical air filter that's fairly dense so air isn't pulled through it unless the regular one is somehow clogged. This one you install at a high point in the middle of the piping.
AEM makes one:
http://www.aemintakes.com/search/product.aspx?Prod=20-402s