The Squaxin study above is looking at freshwater habitat use, which is a good thing to understand, but it is pretty clear that the main problem right now is in the marine environment. Deschutes coho smolt production is well-correlated with the number of adults that return and that adult to smolt ratio has not declined during the recent population crash. However, survival after the smolts hit the saltwater is a fraction of what it was in the 1980's.

That run used to withstand extremely high exploitation rates, and still managed to maintain several thousand returning spawners. Once the marine survival went down, even reduced harvest rates were not enough to keep the population from crashing.