Water in floor of driver's side E39.
I've had a problem with water on the driver's side floor after rains. After partially removing the headlines and checking the sunroof drains I continued to experience a wet floor.a Several posts mentioned cleaning the tube like drains off of the cabin air filters. I did this to no avail. After further reading, I found there are two set's of drains on the cabin air filters, one tube-like drain that is part of the housing, and another underneath the housing directly in the sheet metal underneath the brake fluid reservior. This is found by removing the cabin air filter housing to reveal the area. Mine was "flooded" with about 4 inches of rainwater and the finger sized hole at the bottom was clogged with leaves. if you are having this same problem with water in the cabin, check this first. Much easier and simpler than the sunroof route. It's still not clear to me if there is a similar hole/drain on the passenger size assembly which holds a box of electronics.