Found an easier way to do it rather than type in river names and find what you get.
Go to (fish stocking query):
http://a100.gov.bc.ca/pub/fidq/stockedSpeciesSelect.doSelect Atlantic salmon under fish species, and Province of BC and hit select.
That will generate a list for you of every system in BC that has at one point been stocked with Atlantic's.
Some Island notables:
Ash, Chemainus, Courtenay, Cowichan, French Creek, Englishman, Great Central Lake, Nanaimo Lakes, Qualicum and Sproat (among others).
Mainland notables:
Trout Lake, Stave River, Squamish River, Harrison Lake, Deer Lake and Coquitlam River.
All Atlantic's stocked were diploids in hopes to establish wild, naturalized runs.
None of these runs ever took hold.
This is partially due to the large difference in what Atlantic's are adapted to. The main adaptation they lacked that lead to their demise was resistance to BKD (Bacterial Kidney Disease). Almost all pacific salmon carry BKD, but they have evolved along side the disease for many years and have an immunity to it (unless they are spawning, or already ill). Atlantic's have absolutely no immunity to it, and die with exposure. This, among other diseases, and emergence times all kept the Atlantic's from establishing runs.
Now apparently, some years there are good runs of Atlantic's in the Salmon river. I haven't been up there to catch them, but I hear that they have somewhat started a small run there. From what I understand is they have also observed smolts (easy to spot, very large pectoral fins) in swim counts (although I can't find confirmation of this anywhere). It would be interesting to see if these fish have somehow developed an immunity much like pacific salmon to BKD, or possibly the low salmon returns higher up in the system have helped these Atlantic's along...
Cheers,
Dan