This is a total longshot but something I thought you should be aware of. Since the water is in the side compartment and appears to be from the bottom, it might be coming in from a just inside the bumper. On either side of the X5, right beside where the two side compartments are in the back cargo area, there is a large vent covered with what looks like louvers. This is covered on the outside by the side part of the rear bumper cover. You can see the other side of this when you open up the passenger side compartment and look inside. It looks like a large black grate. (See my PDC retrofit guide on the X5world home page and go to page 14 for a picture of what I'm describing.)

I really don't know if this is the source of your water but something to consider. Broknlgs' suspicion about drain tubes is a good one.

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