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I've not had this on a BMW, but I'd look for two things first.
If you have a sunroof, check that the drains are clear.
Check the area below the pollen filters under the bonnet. If the drains here are blocked, then the air plenum chamber fills with water until it overflows into the heater and into the car.
Looking at your location, and your recent weather, this is a favourite. The heater air intake/plenum chamber is prone to filling with leaves, which drop under the pollen filters and generally block things up. If this is the case, there will be a LOT of water in there!
Remember the Rover 75/MGZT? When they fitted the BMW diesel in there, they fitted the ECU in the plenum. Problem was, when the drains blocked (which they did as the pipe was a small bore), the plenum filled up, drowned the ECU, shorted it out and caused large bills!!
Mike
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