Never had low coolant message except when I drained the rad and block. Think you are in a soft water area so tap water should be OK for now. You got to do the obvious-check for leaks first. Check the hoses and see if you have any drips on the sump guard. Look for mayo under the oil filler cap but that can also mean its running cold. You can have the cooling system tested but I'd be doing a compression test first. To be honest, if your coolant looked black I'd def be worried but not with the tiniest bit of gunge in it.
Oct '00 E46 330i. Feb '92 525i (departed)