I have the dreaded water in the spare wheel well problem. I've never had an issue before but this past spring I cleared all of the sunroof drains as preventative maintenance so I think they're OK. The first place I can find the water is on the right side of the car in a lip/tray just inside the tailgate seal in front of the bumper as per the photo below.



(Any water that's on the seal is from my mopping it up.) I can't find any signs of where the water is getting in. There are no signs of a leak in the tailgate itself or in the seal between the glass and the tailgate. There's no water in either of the storage trays behind the rear wheels.

Any suggestions on where to look will be gratefully received!

 

I'll tell you how I checked my 4 drains... The front two drain by the door hinges, so with the doors open, you can easily see how quickly the water flows out.

For the rears, I park the car on an incline, then get a cup of water and pour it into the outer sunroof rails, towards each drain. I've placed an empty, same size, cup under where the water should drain behind the wheel, and see how much water I get back out, and how quickly. That's how I determined that even though my right drain wasn't totally blocked, it was flowing way slower than the left one. So I ended up grabbing its end, and clearing it, and then repeated my test, and it was perfect.

Make sure you rule out your drains for sure, instead of assuming they're ok...
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I agree with Lotus, if you havent yet, check those drains carefully. And please post a pic of your E61 M5!!!

 

I checked the drains and they're running pretty clear. Another bout of heavy rain overnight and more water in the same spot.

 

And the required piccie

 

Nice piccie!

 

Finally found it. Water runs down the channels under the tailgate into which the gas struts are recessed. At some point the water gets under the seal and emerges on the inside of the seal. Imagine the cross section of the seal as being a narrow upside-down U with a tube on top. The U-shaped portion fits fairly tightly over the body flange and the tube acts as the seal. The water is effectively going down one side of the U and up the other.

I did remove the seal over the summer. There is some sort of glue or sealant in the "U" which I didn't replace - silly me. Any ideas what should be used?

 

I've been getting a little water in the passenger-side storage compartment after a heavy rain or if I hit the sunroof with a little too much water when I wash it. I did a drainage test on the rear drains this afternoon, and the passenger side is definitely partially block. How did you access the end of the drain, Lotus99? You say you ended up "grabbing it's end, and clearing it". Thanks!

 

I pulled the facia back in the car rear compartment, located the hoses both sides. visualised them from under the car. Pulled the hose clear and cut the filters off. Replaced them and pulled them to the place visualized under the car. I blew them out with a large syringe and water bottom to top. Then i poured water into the moon roof cartridge rails on both sides till it ran fast and clear. No leaks for a year plus now.

 

I looked inside the passenger side compartment and could not see how to access the drain hose. So I got the car pretty high up on the lift, and I removed the plastic under-cladding on the passenger side. Then I shined a flashlight underneath the rear corner of the car, just inside the bumper, and I could see the end of the hose with the valve on the end of it. I got a long pliers and reached up behind the bumper and pulled the valve off the end of the hose. The driver's side had enough room to get my hand up there, so that was even easier. Taking the passenger side under-cladding down also gave me the opportunity to clean all the stones and mud that accumulated underneath the compressor for the rear air suspension. So that project is finally done.