Draining problem

After a rain storm my car doesn't drain very well and the water ends up soaking my floor's carpeting. It's not so bad as when I first got the car and didn't know about the drain plugs in the bottom, tho....woke up one morning to about 10 inches of water in my car :eek:
Anyways, I've left my drain plugs out since that time, but never seems to drain properly. Any suggestions?