Most probably the drains for the area that is coverd by the plastic tray are blocked and water pools up and enters the car this way.

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'88 Golf 2 1.8 GTI 16v PL(project)
'01 Passat B5.5 1.9TDI PD
'95 Passat b4 1.9 TD (RIP)

"Cornering perfectly is like bringing a woman to climax.” - Jackie Stewart