Well you should probably post the question in the X trail section, but still welcome to the forum. Do you know if you have a T30 style or T31 Xtrail? I know on the T30s the last section of the roof rail can work its way loose, and water gets in through there. You can tell if its getting into your wheel well, and simply by lifting on that section of the roof rail to see if its loose or even comes right up and off easily. Dont worry you can put it back in place. It just means the bolt inside holding it has come off.
Otherwise, the problem is probably a tear in the rubber seal that surrounds your rear boot opening. Check it for tears. They are just pressed fitted on so if yours is bad you can get a new one from a dealer and change it easily yourself.