I Had the same thing happen maybe 2 months ago after a bad rainstorm, as soon as i pulled forward i heard the water and was like wtf is that. Had to rip the interior out as well as the seat and sucked out maybe 2-3 gallons of water.

Turns out it was the drains below the windshield collar. Just simply remove it, unplug the drains as your all set. Weird thing was there was a rock in one of them that was bigger than any opening to originally get in there.