On several occasions I've noticed that there has been loads of water in the boot, under the removable flooring. After the recent heavy rain, this was really bad!

Any suggestions on where it could be coming in from? Seals look good all around, and the boot floor isnt wet, so can only assume it's coming in from underneath somewhere....

For me was coming from the side air wents. See pics. I quick fix would be to remove the two plug from the bottom. 

My wife’s car developed condensation internally. We could not find the source until we lifted the boot spare wheel lid. The spare wheel well was full of water. When we checked, the rubber expandable conduit  running between the actual body of the car on the top of the tailgate into the tailgate was lifted slightly off the body of the car, so all the water running off the roof, instead of running down the side of the tailgate and off the car was running into the car and down into the well where the spare tire should be. It just required pushing back in firmly so that it sat properly.