I had water in the rear footwell of my 2004 Mondeo and was easily fixed. The water came in though the horizontal window weather strip ( where the window slides up and down ). Even a brand new weather strip will not stop all of the rain water getting in. It hits the SPEAKER and drops INSIDE the sealing rubber at the bottom of the door frame then fills the footwell.
All you have to do to fix it is to remove the door inner panel ( 5 minute job ) and with a hose pipe you will see the water dripping in above the speaker. I found a roll of 5 inch ( single brick ) damp proof membrane in my shed. This is thick plastic but any thick plastic sheet will do. I cut 3 lengths ABOUT 16 inches long X 5 inches wide. The speaker has 2 studs at the top. Make 2 holes the same width as these studs at the top of the three 5 inch strips.
Or just cut a fan shaped bit of thick plastic sheet 5 inches at the top X 16 inches down and about 12 inches wide at the bottom.
Remove speaker, then position the 3 plastic strips ( LIKE A FAN OPENING WIDER AT THE BOTTOM ) at the top of the speaker on the studs so that the water does not touch the speaker but runs over the strips like a raincoat and ends up on the outer part of the door panel and then drips out of the normal hole at the bottom of the door.
That is all I did to fix the leak on one back door but I am sure all doors can be fixed the same way.