Another common cause for water collecting in the rear wells on left and right sides is the sunroof drains.

Search on here and I bet you will find some info. I had that problem on my 2001 E53 when I first got it. Hoses connect each of the 4 corners of the sunroof opening to drains, two at the front A pillars and two at the upper corners of the rear hatch opening. On my car, the rear hoses had apparently shrunk after 13 years of heat, and when they shrunk enough, the hose pulled off the attachment at the sunroof, so water would just pour onto the headliner and drain into the rear corners (depends on the angle you are parked at, I guess).

Separately, I did at one point have an opening back there that was letting water in. Solution to find it was to get everything completely dry, get inside the car, everything really well lit, and have a helper spray a hose from the outside. Was able to then see tiny drops of water coming through. Once found, easily sealed with caulk, RTV, whatever you want.

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2001 X5 3.0i, 203k miles, AT, owned since 2014