Get one of the water resistant prefilter covers like this one http://www.autoanything.com/air-filt...A2582A0A0.aspx it should help, but it's no guarantee.

 

I couldn't imagine how water would get to your setup unless you drove through a lake. I've driven mine through some pretty bad storms and flooded roads with no problems. The first couple of time I always checked to see if the filter was wet after I got done driving, but after checking it 3 or 4 times and it being bone dry, I stopped worrying. Mine's been on my truck now almost a year with no problems..

As a reply to an earlier statement on it being a "Hot Air Intake" if it doesn't have a heat shroud, according to my Edge tuner my stock intake would normally run 30-40 degrees above ambient air temp. I did see it get almost 50 degrees above 1 time. With my DIY CAI it averages about 10 degrees above ambient, and the hottest day this Summer I was out driving, Ambient temp was 103, and my IAT sensor was reading 115 driving down in the city..

My setup:

 

how the f did you get water in there? I wonder if it came over the top between the hood and the fender instead of from below.

 

It was wet it was dripping when i got home. The top of the wheel well was wet as well and pretty much everything under the hood was soaked.

 

Well, if you drive through a deep enough puddle, you can even suck water in through a stock air box. Sounds like it might have been an isolated incident. I say leave it alone for now, and see what happens the next time you drive it in the rain. If it's a good downpour, when you get home or somewhere you can check it, see if it's wet again. If so then you need to figure something else out...

 

But I did hit the water at about 40 mph so that my explain the crazy amount of water all over everything. I might try that filter cover though.