if you have a sunroof you have two drainage lines for it that run into the trunk next to each wheel well
these lines tend to get clogged or pop out and then leak into the trunk

if it isnt those then check the tail lights
the seal around them is prone to leaking, also if the lense is cracked it will leak as well (such is the case with mine)

if those dont solve it then do this
pull out everything form the trunk, spare tire, carpet, etc...
dust all surfaces with chalk or flour or some other light powder
either wash the car or drive it in the rain or do whatever you can to get it to leak
the powder will show the path of the water as it leaks

good luck