If you have a sunroof there is a tube that runs from the corner of the assembly down the apillar and dumps down next to the door. Mine had wiggled loose once and cause water to come in. Also like previously mentioned there could be a bad seal around the door, and also I have had water come in between the window glass and the rubber seal on the door. Also make sure the holes on the doors bottom are not plugged trapping water inside. Also if you can get under the car you can see 4 plugs underneath where the seats are and sometimes the factory glue lets go and they pop out creating an inch and a half hole that condensation can get up and into your car through.
Same as Jaaquo, i have an 02 focus, when i had a puddle of water in my pasenger footwell a couple of years ago, it was due to the seal having perished between the windscreen and the cover over the air intake, which meant water was easily running straight into the car. I resealed it and its been fine up until recently when the seal has perished again, meaning another repair jobby.