As long as you have the skidplate under the car and the inner tire fender well yuo'll be fine as long as you don't drive into a DEEP puddle that you shouldn't drive in anyways. I've had my CAI for years in multiple states and when it rain here in AZ IT RAINS! You shouldn't have a problem with a true CAi, but if you're really concerned go with the SRI. Even a warm air intake is better then the factory crap.
2006 Focus ZX3 SAP, Draxas Header, FS Werks Flex pipe, MBRP exhaust, CAI, Tuned, Debaged, tinted windows, FRPP lowering kit, SVT 5-spoke wheels, Black Halo Projector Headlights, Niteshaded Side markers and tails, Mazda rear wiper, mustang antenna.