Weep holes may be plugged...
You may want to check if the weep holes in cavity in which the convertible top is stored are plugged. Plugged weep holes are a problem for E46 convertibles. By design, water is supposed to drain through these weep holes in the E46's convertible top storage cavity.
I had this problem. It manifested itself in standing water under the rear seat, in the rear seat foot well and in water in the spare tire cavity in the rear trunk. This occurred after even the smallest rainstorm. I think I head 10 or so inches or water accumulate in the trunk. A real pain in the neck.
One way to check if you have a problem is to put the top partially up -- allowing access to the convertible top storage cavity. Pour a small amount of water into the top cavity near where the top mechanism is mounted to the body on each side. If the weep holes are plugged, the water will just stand there -- or drain painfully slowly. If the weep holes are open, the water should drain quickly and exit through drain lines beneath the car. You need to do this test on each side of the convertible top. If this water doesn't drain away, it works its way into parts of the car, causing standing water...
If the weep holes are plugged, you can take it to the BMW dealer and spend $2k to get it fixed. Or -- you can follow a procedure that I found elsewhere on this site. I had the problem fixed in about 3-4 hours of work. Needed to buy or borrow a couple of tools -- and it takes two people to do it -- but well worth the effort.