Our X3 has just had the same problem. Water in the driver side front and rear footwell.
The 'no water' warning came up on the dash so we filled the water resevoir up (in engine bay). Later that day the no water warning light was on again and the resevoir was empty again.
A quick check showed that the front jets worked fine but the rear jet didnt. No more than a trickle to rear jet despite having water in the resevoir.

The car was under warranty so we took it into BMW who confirmed that the pipe to the rear jet (shown in the link Goldstone added in last post) had come apart at some point between front console and the back of the car.
BMW had the car for two days to do the work as they needed to get the console and all of the trim and seats out to get to the pipework and check the whole length for the break. Getting the carpets out also speeded up drying them out as they were soaking.

HTH.