Couple of things to try:
It might be the rear seat latches - Fold the seats down and if the rattle disappears, it's from the latch. This was an issue in the earlier models but haven't seen it recently. Easy fix is to wrap the latch bar with some electrical tape. Also, the leather rubbing can be annoying and I've read using leather conditioner helps
Other rattle might be coming from the top hatch. On either side of the hatch are rubber stoppers. Loosen the torx screw that holds the stopper and rotate the stopper 1/2 to 1 turn out, then re-tighten the screw.
'03 325i OrBlu, MT, PP, SP
'01 X5 3.0 AlpWhite, AT, SP, CP
'89 325i Bronz, AT(retired)
'02 325i StlGrey, AT, PP, SP
'13 328i AlpWhite, AT8, Xenon, HK