I just had this happen to me. I was cleaning the car and suddenly the shop vac started sucking up water in the rear passenger footwell. Fortunately, this is very common. The water enters the interior of the door where the bottom of the window meet the door and this is normal. There is a vapour barrier on the inside of the door panel that is a thin foam material sealed around the enges to the door. The idea is that water reaches the inside of the door, runs along the vapour barrier to ta a drain hole that directs it to the bottom of the door where is drains out. In my case, the seal from the foam had failed and the water ran to the inside of the door panel and into the foot well. Theere was mold starting to build up on the door panel. Do some searching for vapour barrier on bimmerfest and that will get you into the right direction. My BIG work of advice is to peel the old vapour barrier off carefully and head to your local dealership and ask NICELY for some adhesive. The parts guys might have to ask a shop mechanic for what you need. It comes in a roll and there are about 5 strips on the roll. You need about 3 feet and you can piece the adhesive around. It needs to be a continuous seal. Do not listed to the fools at Canadian Tire. They sold me goop which did not seal and just ruined the vapour barrier and I had to buy a new one at $65.00. You can re-use the old one as long as your carefull removing the old adhesive.
Once you have replaced the vapour barrier, leave the door panel off for a couple of days to test your fix and to allow the door panel to dry out completely.
PM me if you run into any problems...I did mine twice.
2003 530i Titanium Grey/Black, Premium and Cold Weather Package, Ultimate Pedals, iceLink iPod Kit, Bluetooth, M5 Deck Lid Spoiler, M5 Rear Sway Bar, M5 Dead Pedal, DINAN S1 Trans and Engine SW, BSW 12' subwoofer, Valentine V1 hardwired, SMG Paddleshift kit
2005 X5 Sterling Grey/Truffle Brown, Premium and Cold Weather Package, DICE iPod Kit, Bluetooth, DSP, Comfort seats, Invision DVD Headrests, Valentine V1 hardwired, TomTom GPS