Deer Creek probably has the best-known run of native summer-runs. The Sauk also has a small run of native fish. The Cascade River run is a mixture of wild and hatchery stocks. Historically, the North Fork of the Skykomish and the Tolt had small runs of native fish, and I believe I recall reading somewhere that Finney Creek on the Skagit once had a run that has probably been driven to extinction by destructive logging practices in that watershed. The summer-runs in the Green, Snoqualmie, Skykomish and North Fork Stilly above Deer Creek, are Skamania stock from the Reiter Ponds facility, which is the best argument I can think of for somehow obtaining permanent funding for that operation.
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PS