I am jealous of your M54 and it's cheap and easy to replace water pump.
However, don't guess. Do you have a coolant pressure tester? A forum member on the E60 subforum recommended one to me when I was having trouble identifying a coolant leak. This is the one I got. I can't get over how useful it's been. I've used it a ton and don't know how I lived without it. It's great after doing coolig system overhauls to identify any leaks before filling the system up.
However, don't guess. Do you have a coolant pressure tester? A forum member on the E60 subforum recommended one to me when I was having trouble identifying a coolant leak. This is the one I got. I can't get over how useful it's been. I've used it a ton and don't know how I lived without it. It's great after doing coolig system overhauls to identify any leaks before filling the system up.