This is what I was dealing with before I put a new top on. Every time it rained I had to end the drive by getting into the back seat and towel drying the whole back end where the top lays down into. A new top corrected this issue for me.
Now if you have water in the rear seat floor then you might also check to see if you rail drains are clogged. The whole system is designed to leak to a certain extent and just let it all drain out the bottom - the drain is in front of the back wheel in the pinch weld. I cleared mine out by sticking a small drill up into it and moving it around.