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Hello,
I have my Jazz 2003 1.2 for 2 years and now when I checked spare wheel I found about 2 liters of water in this space.
I tryed to find how is this possible and I found this (attached pict)
The paint was fine and after I cleaned this area on top with a damp cloth the paint disappeared and this "putty" showed. Is this a standard filler for this location or is it just me and will this be the cause of the problem?
Very common problem. The seams have sealant from the factory, but it degrades and cracks with time. Apparently there should be further spot welds within the bodywork to hold things together better too. You could remove the interior panels in the boot and look for water stains (don't reinstall them until you're sure the leaks are fixed). A few drops of different coloured food colouring around the body may help pinpoint where the water is getting in.
You'll need to clean off and replace the sealant, covering all the cracks and seams around the hatch hinges. Sikaflex 221 is probably ideal (I used Flex Glue and it worked but is degrading after a few years). Make sure you lift the rubber gutter liners on each side of the roof and re-seal under there as well (the cracks often extend under there too). I also found that some water was getting in behind the brake lights. People have also reported water getting in through the bolt holes that anchor the hatch struts. The doors are known for leaking too.