Elmtree,
I'll tell you what I know.
The Nisqually has been in serious decline for over a decade. This was one of the rivers I learned the ropes on back in the early 80's when it was still good. Even then, reports from the old-timers were "it's not as good as it used to be." But, there were fish and in enough abundance to go with confidence that if you put your time in, you were going to have some action. Like many rivers that get hammered, the fish "held their own" so to speak and always returned in fishable numbers. That was up until the mid to late 80's.
Then, numbers suddenly dropped sharply one year(don't remember exact one)and the usual "they're just late" became the norm. It's never been the same since. As I remember it, The drop was drastic enough that not even indian netting was blamed for the decline because the netting was somewhat regulated. There was specualtion that something else was happening. Habitat wasn't the main issue because the nisqually is still a wild river albeit below alder dam. But, that's alot of usable area. I remember reading that WDFW suspected a virus of some kind was either killing eggs during incubation in the gravel or at some point when the fish were young. It was a theory as I recall and WDFW kind of drifted off in the mist as afr as informing the public.
Maybe they are as clueless to the cause of mortality as they were back then. Or, if they know, perhaps they have no cure if it is a virus. You probably shouldn't take this account as absolute fact but that is the way I remember it and I'm am probably off on a few points but I definitely remember news of a potential lethal virus.
Too bad, it was a great river at one time. If any WDFW personnel read this I would really be interested in being brought up to date on the status of the Nisqually. What do you know?