Last winter and again this year I have opened my car boot to find it drenched. The carpet is soaked and the wooden lid to the spare wheel wet through and rotten.
There was nothing in there that had leaked and I assumed it was the rubber seals to the boot. I took it to the garage and they said selas were fine but put it down to a faulty rear windscreen washer tube. They fixed it and all was OK until now.
A year on and the same thing has happened. I opened the boot yesterday having used it regularly and its sodden again. Its a 2003 VW Polo.
I had the fiesta from hell with a similar problem, only the mystery leak filled the driver and passenger footwells. Seals changed, all sortsa things done - never cured it. I used to just hoover the water out with the coin-op vacuum machine at the garage. Someone seriously suggested drilling a couple of holes through the floor, but I never did that.
This how I would check, remove the rear parcel shelf and get someone to run water over the rear windscreen with an hose pipe while you are in the rear of the car and look for any water dripping through.
Used to have a Rover SD1 years ago and every time it rained the spare wheel well would fill up with water, got fed up having to keep emptying it so in the end I just removed the rubber bung from the bottom of the wheel well and left it out so that the water just leaked out.
as a bodyshop when we get a water leak problem we actually put someone in the boot/tailgate area (usually apprentice)and put a hose on it...99 times out of 100 its fairly obvious.
Not sure what sort of garage you used but a bodyshop is more familiar with water leaks it could be bad sealing on a welded joint which is what happens in Fiestas Mosaic
When you look at the tail gate itself, look around the sides / top & check that the gap in the tailgate is near enough the same all around Maidup, also, loo into the spar wheel well & the sealing joints ( welding joints) the joints at times are sealed with body sealant, put a hosepipe under the car & direct the water flow UPRIGHT from the base of the boot. this was once a problem with a 405 Peugeot I had a few years ago.
we have this problem but it is the back seat foot wells have puddles in after heavy rain, we are unsure where the water is coming in but sure it is not the sunroof, we hoovered it out with a garden hoover and it stinks as not getting time to dry out, I think it could be the door seals?? It is a Toyota carina
Chess, in some cars you have a thick under felt, once that gets wet it's very difficult to dry, on the floor of the car beneath the carpet you have channels where the water gets trapped, there are Rubber plugs beneath the carpet but the are sealed, for you to dry the carpet out properly you need to remove the seats + the carpets, in your case I would lift the rear seat base & check for corrosion in the bodywork, other than that, what has been already said.
I've removed the carpet and thrown out the wooden "lid" to the spare wheel well. Over the weekend I have managed to dry things out a bit, couldn't see the wood from the trees when it was so drenched.
Now its dryer I can see that the area around the light fitting is still damp and the water beginning to pool again in this corner. Its a completely sealed unit and I can't see any way in, so I'll keep carpet out and a mop at hand until I have time to take it to a garage.