Hello, I hope the following is of assistance.
The most common cause of water ingress into the rear foot well of Mondeo 2001 to 2007 is a fault with the door foil on the rear door.
The doors on the Mondeo are designed for water to run through them and out of the drain holes at the bottom, the problem with water getting in comes when the sponge foil behind the interior door trim fails, this allows water to run out behind the door trim then run down and out of the trim into the car. The foil can fail either due to the sealant that bonds it to the door failing allowing the foil to come away from the door, or the foil has been removed to carry out work on the door (usually a new latch/lock) and has torn when trying to remove from the bonding on the door.
The quickest way to check for this is to have water sparayed onto the door area and look inside for signs of water dripping from the bottom of the interior door trim inside the car. If the foil requires replacing then you need to remove the interior door trim.
If any other areas of the car are wet then the source of the ingress may be elsewhere, if there is water in the boot area check that the rear lights are sealed correctly. If the passenger side front footwell is wet then check that water isn't coming through the pollen filter housing, make sure the trim at the bottom of the windscreen is fitted correctly.
Start with these points, let me know if I can assist further or if you have more questions regarding this and I'll reply as soon as I'm able to.