Puget Sound and the Columbia basin have had a lot of alterations to natural water flow and ability of anadromous fish to ascent the rivers because of dams. And it is very unlikely that those dams will be coming down. Before folks go ballistic on the current administration, keep in mind that these fish blocking dams were built long before this administration was in office and most were built when the so-called "fish friendly" federal and state administrations were in power. These dams that have blocked anadromous fish (or made it much more difficult for them to get over them and upriver or through them and downriver) have had a detrimental effect on fish runs.
Keep in mind that the governors of both Washington and Oregon were opposed to the extra water being spilled over the Columbia dams this summer, and both are supposedly "fish friendly". There is also the problem of whether policy ought to be formulated by biologist, politicians, courts, or interest groups.
Regarding the dam spill this year (which environmental groups hailed as a victory for the fish) were considered by the biologists not to be the best way to insure the survival of the maximum number of fish in low-water years like this. The biologists were of the opinion that barging in low-water years was best. Of course, the opinnion of the biologists working in the Columbia basin was ignored because emotionally, it didn't make sense. Afterall, fish need water and if more water is spilled over the dams, the fish have to benefit, right? The opinion of the biologist didn't fit this type of emotional reasoning, so they were ignored and the judge ruled in favor of spilling the water.
Commercial over harvest and sportsfishing over harvest have also been detrimental to fish run sizes. Plus, there is the ocean, over which we have precious little control, that plays a significant role in the relative abundance or lack thereof of the fish.
Then there are things such as the Mining Act of 1872 that Congress (regardless of which party has been in control) has been unwilling the change or eliminate, which also play a role.
And we must not forget that a Circuit Court of Appeals ruled 3 years ago that only things that have demonstrated, actual value can be considered in the economic value portion of a plan or designation of habitat, and it was upheld by the Supreme Court when it refused to hear the appeal by NMFS and the Forest Service of this ruling. Thus, NOAA-F and other federal and state agencies can no longer include the value of recreation unless they have hard evidence of the actual economic activity (i.e. how many dollars were generated) of that activity. This has had a majoy impact on these agencies.
There are a lot of factors involved: court decisions, legislative, interest groups (environmental, conservation, agriculture, power generation, logging, mining, and development), media, and fisherman (sportsfishers, tribal, and commercial). And we can't ignore any of them because all of them have an impact on the fish. Eliminating those areas that never had anadromous fish from the areas deemed "critical habitat" for anadromous fish hardly constitutes the sky is falling and the fish are losing even more rhetoric I've been reading from environmental groups. Simply put, doing so is emotional reasoning and as such, does not help find solutions to the problem of declining runs.
Items such as the WA State legislators or governors getting rid of sportsfishing and/or conservation friendly Fish & Wildlife Dept. Directors or Commission members cannot be ignored or put on the back burner because they are not as "big" emotionally as changing critical habitat designations. I've seen virtually nothing about this problem from the environmental groups. Likewise, fish farms can't be ignored. Nor can things like: irrigating what used to be high desert to grow grass or alfalfa for cattle (like in the upper Klamath) or holding back water to save fish that has thrived only because of the irrigation dams on the Klamath, while the native anadromous fish suffer from a lack of water in the river; or the dams on the Deschutes used for power generation and irrigation (although then we need to have electrical power generated some other way, perhaps nuclear).