I have a MY00 wagon and went to remove the tool kit from below where the jack is stored (passenger side boot cubby hole), and it appears to have about half inch of water at the bottom...does anyone know if there is a drain hole or plug that can become blocked in that area?

Cheers,
Ian

 

Almost certainly your rear light clusters leaking. Try getting them out, cleaning them up and re-sealing with fresh gunk. A search should reveal the exact procedure. Mine were done under warranty.
Or let Subaru charge you a fortune in labour for doing it.

 

Thanks Pastor, what exactly do I need to look for on the light units (apologies if this is a silly q!)

 

Try a search for leaky rear lights or similar and you should hopefully find a thread telling you the exact procedure.
What happens is that the black gunk (which doesn't set) used as sealant (covering the light units) fails and water gets in. To get at this you'll need to undo all the screws (can't remember how many) and then you'll find the light unit won't come out. this is because the gunk is holding it in. A hairdrier blowing warm air should free it up a bit and let you remove them. Then clean off all the black gunk and use some replacement sealant liberally. Hopefully this will work.
Should have added before doing any of this climb in the boot of your wagon and get an assistant to wield a hosepipe or watering can at the rear of the car while you watch where the water is coming in. That way you can rule out the boot seal or where the spoiler is attached to the boot. 2 other well known sources of leaks.
I'm sure someone on here knows more than me, let's hope this thread catched their attention.