At one time I remember there seeing an in-line valve that you could put right after the throttle body. The premise was that if your intake sucked in water, the pressure difference needed to pull that water into the intake would allow the valve to open so the valve would act as the new "inlet" for air.... think about it this way, if you clogged the intake, this valve would open, and water being sucked up is kind of like clogging the intake except the engine is capable of creating enough vacuum to pull the water all the way in.

I saw one a few years ago but haven't been able to find it recently.