Within nearly all drainages occupied by Onchorhyncus mykiss and O. clarki there has always been a portion of the populations of these two species that we would call "resident."
These non-anadramous types are today typically found in waters seperated from their anadramous brethern by physical obstacles but not in all instances. They may also be seperated by choice of or time of use of anadramous spawning and rearing areas. The most likely cause of their decline is catch and eat fisheries regardless of method. I remember the public meetings when the state first proposed flyfishing only waters and reduced limits on trout in streams....Guys came out of the woodworks saying in the old days they would catch and take home trout by the bucket full, had been doing it for generations, and were pissed that they couldn't continue to do it. As for correlations giving an answer blaming one specific possible cause....well have you ever heard about the correlation between dog bites and sunspots?