I am currently in the process of buying a 2003 Alero. It has the problem of the water going over the box and floor. they had the windshield replaced, the rubber all replaced. But no luck. Well, I called my mech, he knew right away what it was. Will run around 200 or so to fix. The water is coming in from the backup of the drain tubes by the wipers. They run down the car to clear any water.. But instead of the water continuing to go through the drains have been clogged with maybe sticks, leaves, etc. He has seen the problem several times and is a constant problem on some cars. So you need to find someone to clear out the drains running down near the wipers. There is a drain that goes down each side.
Hope I helped. I was not going to buy it because of that, but amazingly, my mechanic knew right away and knew who could unclog them.
littlechi