Larry -
You asked the question of what has changed?
The first as others have mention is the human population. Since 1980 the population of the State has increased from just over 4 million to about 7 million. 80% of that population live in the Puget Sound basin. We are all familiar with the long list of problems associated with that population growth.
The number of harbor seals have increased 10 fold since the marine mammal protection act. The numbers of harbor porpoises in recent years have increase from virtually none existent to now they are as abundant as harbor seals.
Because of the location of the Nisqually in relation to the Snohomish it should be clear that fish originating in the south sound are exposed to more and for a longer period of time the cumulative impacts associated with those changes.
One factor that is not commonly talked about is the changes in the regions river discharge patterns. Because of climate change (we will leave the cause of those changes to another debate) the timing of the freshwater discharge from our rivers have changed; and in some cases dramatically. Historically much of the freshwater entering Puget Sound was the result of snow melt which occurred in the spring/early summer. That large freshwater input increased the mixing of the waters of Puget Sound which coupled with the sun light of longer days drove a significant pulse of productivity. Today we see more of the run-off from floods/freshets during the fall and winter period and less snow-melt in the spring. The result is fewer and smaller productivity blooms at the critical time that smolts are entering and migrating through the Sound.
Curt
Again, I was trying to focus on the rather short term decline in smolt survival from South Sound. Your observation about changes in fresh water flow timing is interesting as is the possible impact of parasites.
The link I posted includes a page showing increases in population of seals and harbor porpoise but then goes on to suggest that just because there is a correlation does not mean a cause and effect relationship.
Information which was promulgated during development of the state's Puget Sound Rockfish Recovery Plan indicated that harbor seal population in Puget Sound around 1970 was approximately 200. Current estimates run between 15,000 and 17,000 consuming between 25-30 million pounds of food a year. And while I doubt there are 15,000 harbor porpoise they definitely have increased and now we have a significant population of California sea lions and a small but growing population of Stellars all of which have to eat although the sea lions probably not on smolts.