Sun Roof

If you open the sunroof you'll see a drain hole at each corner. Do not force anything down the holes and push hard. If you push the drain pipe out you'll need to remove the headlining to reinsert it! Better idea to put a funnel into each hole and pour in water to make sure it's not blocked.

I'd also check the sill and door drain holes are free.

On my two door E36 the window rubbers on the rear windows used to ride up and need pushing down every now and then.

While it may be the sunroof, unless you are absolutely sure you should also check for this common problem.

Inside the door panels is a seal which directs water which seeps in past the window seals down to the bottom of the door at which point it is supposed to exit outside from the space between the door and sill via drain holes. Over time this seal can fail (it's just a big piece of plastic which lines the entire door panel). When this happens water accumulates in the rear foot wells. It is very difficult to spot, because you will never see a stream, especially with black carpeting. It just seeps down and floods the floor.

Might be worth checking. To do this you have to remove the interior panel and check that the plastic is SEALED all around. An easier way to check is to get a large piece of plastic (like a big garbage bag), an put it on the inside of the door so it goes from about the middle of the door and DOWN AND AROUND THE BOTTOM OF THE DOOR. The bag should be visible from the outside sticking out between the bottom of the door and the sill.

Every time I went through a (touchless) carwash, my passenger side back seat well was FULL of water. After I dried it out I tried this test and went through the car wash again - no water. Replaced the seal and all was fine.