I had same problem with my car drains were blocked below windscreen under brake servo this was full of water and the water was running down the bonnet release cable Ito the inside and running Down the back of the carpet after rain behind the front seat they were 100mm water also check drain into the inter wing this was blocked with leavesSeveral options to test, all DIY with basic skills.
1. Check beneath the pollen filters that the drainage channels aren't blocked, this is quite common on 6 and 5 series and if one/more is, clear them.
2. Check the rear window seals (get inside and get someone to play a hose on the outside).
3. Check the rain drains on the bottom of each front door aren't blocked.
4. Take the rear seat out and see if there's water beneath.
Try these first and post back if unsuccessful - remember, water runs to the lowest level so the actual leak need not be near the water pool!