CM -
As you know habitat of a given river basin is quite complex and each of our anadromous species partition the habitat resulting each species developing different spawning and rearing strategies to take advantage of specific habitats. Because of those different spawning and rearing strategies it is common for the various species to have different production bottle necks.
The fact that a given species is doing well in a basin is doing well does not mean that the basin's over habitat is not degraded only that the most critical production bottle neck for that given species is less degraded.
Let's consider the case of Skagit bull trout. The key habitat for that species is cold water spawning habitats (for egg incubation) and quality juvenile habitat. In the case of the Skagit bull trout that essentially cold water spawning locations is found in the head water areas of larger basin tributaries. Fortunately for those bull trout it has been estimated that 80% basin key bull trout habitat is still essential intact (located in a national park and wilderness area. It should not have been a surprised that once harvest pressure on bull trout was relaxed that the population increased.
Contrast that with the situation for Skagit basin winter steelhead. The vast majority of the 290 miles of steelhead spawning habitat is located well downstream of that key bull trout habitat. Much of that potential steelhead habitat has been altered by man that significantly have limited the over-winter habitat (complex habitat structures) for both the fry and parr steelhead. This altered habitat limits the steelhead potential of the basin below historic levels.
Similarly habitat changes will effect each of the basin salmonids populations to varying degrees .
Curt