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Typically cabin filter housing is installed incorrectly, check that. Windshield cover should be over filter housing, not below.

This is very fun on winter, driving on icy road and booster is full of ice->no brakes!
 

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Just FYI about brake booster... My booster got flooded too. Same result and experience.

Fast forward 2 years. Now, especially when I first drive the car in the morning, there is a dead spot in the booster that i notice when i get on the freeway... and it is getting worse. My thought is that over time the portion that was wet and then eventually dried, did not and usually will not return completely to normal. It gets brittle. The diaphragm portion of the booster seems to no longer totally seal the vacuum anymore.

Additionally I think that this effects the engine somehow. Not sure how but I feel that screwing up caccum harmony has enormous effects in this engine.

Having said this, I will be replacing mine in the near future because the chance of having it not work properly on the freeway could cause my car and someone else's a whole lot of damage. Love my M5 and want it to survive!

So my thought is replace it and never let it happen again. Brakes are too damn important.
 

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Late to the thread but just dealt with this same situation on my 2002 E39 M5. Drain holes clogged and water in compartment and brake booster. Brake master cylinder corroded. Engine rough idle and dying when idling - probably sucking some water. Fortunately, no hydro-locking but apparently close to it. All M5 owners should check this periodically. Local BMW dealer missed this, even with known symptoms, but sharp independent shop picked right up on it.
 

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Add me up. I went to a car wash, and after I left the beast stalled when I hit the brakes. I could also feel water gurgling through the brake pedal. Everything went away the next day and never came back. It happened again the second time I went to the car wash, and again went away the next day. When it happened the third time, I decided to google it, and bingo.Took apart the driver's side air cabin filter, and the brake booster compartment had 2" of water in it.
The drain hole was plugged by debris, I cleaned it out nicely, and washed it down for good measure.
I also sucked out quite a bit of water from the engine side of the brake booster diaphragm and can also confirm this is not enough.
There is also water on the firewall side, which gets pumped to the engine side when brake pedal is pushed in.
I tested this by starting the car and pumping the brakes, I was able to pump quite a bit more water out of the engine side, which was previously empty.
 
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