I had water in my boot, which I noticed because I had mould on my rear seats.
Behind your boot carpet side walls, you have a vent each side of the car, to allow air to escape when you shut the boot. On mine, the driver side was simply missing ( god knows why) and water was getting in here and pooling into the boot.
Id say its unlikely yours is coming from here, but, if you try everything else with no solution then maybe its worth a try. The seals around the vents can perish as well.