When I asked the question "What's changed?" it was primarily directed at the issues on the Nisqually compared to other systems further north - specifically the Snohomish. See the linked I provided and particularly pages 31-40 which provide those comparisons.

Through the efforts of a variety of fishing/conservation groups the Nisqually delta was spared industrial development and the agricultural diking from the early 1900s has been significantly removed/breached to provide more habitat for young fish. Yes, there is a dam on the river but it was put on line in 1945 so presumably any adverse affects became the new norm in the 50s - long before this current smolt mortality phenomenon. And I would opine that population growth in the Snohomish basin has been far greater than in the Nisqually basin. Then there is the relative lack of riparian development what with tribal lands and Ft. Lewis. On the face of it the Nisqually should be the poster child at least in comparison to those other systems.

That said, I had forgotten about the closure of McAllister Creek's facility in part due to infestation. Not sure if it is the same organism identified in the study but if it developed after I-5 that would put it no earlier than the early to mid-60s then possibly migrating into the entire delta. If so, does that undo the efforts to provide that additional estuary habitat? Another Master's or PhD study???