poorly fitted roofs leake every where
when teh doors are shut the glass should sit under the seal
water can get in thru the sills if the drains are blocked but water gets in
to fix it for sure take the seats out take the carpet and the insulation out and dust over it with talc and wait til it rains to see where it comes thru
could be rubbers, floor seams or rot, bulk head gromets, 1/4 windows
many many things