Hi- The tracks technically started off the foot of Cornwall, down by the former barge slip. The area they call The Dry Dock. They crossed under Chestnut and ran parallel to the BN (at that time GN) before crossing Roeder to go up the Squalicum truck route.
There isn't all that much of the Milwaukee left in Whatcom County. You can see where it crossed the Hannegan just before Builder's Alliance, and the BNSF still uses the Sumas to Lynden line on occasion. There is a real cool old trestle in Whatcom Falls Park in Bellingham proper, with some suspended rails over it. It was used by The Milwaukee to get to the Bloedel Donavan Mill, where the park now stands.
If you are interested in the Milwaukee in Whatcom County try a Google search using the name Al Currier. He is a friend of mine who heavily photographed the last couple of years of the operations up here.
Hello! I stumbled upon your post from November 25 and was wondering if you know more about where the "Milwaukee Road" track went. You mentioned that this was the track that crossed Meridian (and went to Canada via Sumas). Where did it start… down by Bellingham Cold Storage? Do you know about any other old rail tracks around Bellingham? Thanks!