Hi all water is lodging at each corner of the boot seal and leaking down the boot lock and into the spare wheel well I have read previous topics on putting holes in the rubber is the best option if anyone has any photos of this being done  thanks. 

If it's sitting on top of the seal it's the exact problem I had with our Kodiaq.  It took me a while to track down the cause having looked at light seals, gas strut fixings and rear hatch seal but the issue was actually the rubber grommet round the rear wiper leaking between it and the window glass, the water then running down inside the interior trim onto the seal.

 

The solution was to reseal between the rubber grommet and the glass with flexible polyurethane windscreen sealant.  It's a bit tricky to do without taking the wiper off but is possible by using a small screwdriver to carefully lift the grommet a bit at a time to allow you to get some sealant under it.

Found similar on my 2018 hatch month ago, water pooling on inside centre of seal dripping down boot lock and into spare wheel well. On mine found the boot seal was slightly loose on L/H lower corner so the water was getting through to the inside, refitted and been ok since.

Thanks guys

Hi all, i have the same issue with water filling up in were spare wheel is. i have a skoda octavia 2013.

if i can fix myself i would but i dont know were to start.

im not sure were to punch holes in the seal so warer can get out?

i had to take buckets of water out under the spare wheel.

the car smells of dampness, probably needs a full valet now.