This is a huge issue for those of us that enjoy kokanee fishing here in Washington.
The Whatcom kokanee were the source for the vast majority of kokanee in this State (and much of the country for that matter). The Whatcom kokanee are a native fish to the lake. If I recall correctly the hatchery on Brinian Creek (south end of the lake) has been in operation for approximately a century, first as county facility and then with the creation of the Department of Game (1930s) a State facility. Millions of eggs are taken at that hatchery every year with many shipped for use in other lakes.
The tribal plans for the Middle Fork Nooksack is to introduce spring Chinook (not coho) above the diverson dam. Middle Fork Nooksack water is divert to lake Whatcom for domestic and industrial use (since early 1960s).
For decades there has been no history of dieseases of concern (virus etc) with the Whatcom fish. The concern is that with anadromous fish getting above the diversion dam the salmon could introduce diseases to the water system. In the past only a relative small number of adult kokanee (a 100 or so) had to be tested annually for diseases of concern since there has been no history of problems. The rub is that with the new potential of diseases policies require that all the brood fish be tested. However as a practical matter that is no possible; either physically or economically. It is often the case 100,000 or more adults will be spawned at the hatchery in a single year and there has been as many as 20,000 spawned in a single day.
Without that testing fry from Whatcom can not be used in other watersheds. That would mean for many of Washington Lakes future kokanee fishing will limited to whatever natural production is now occurring. In spite of extensive searches no satisfactory replacement for Whatcom has been found. There as some isolate lakes that can be used but the kokanee populations are too small to begin to provide the kinds of numbers needed for the state wide program.
Tight lines
Curt