In my opinion the NSIA article is laden with simplistic misinformation and can be considered as little more than propaganda but aside from that it is hard not to see the dams as the greatest obstacle to upper Snake River anadromous fish.

My meager understanding is that while increasing flow rates and creating stronger currents by lowering the reservoir levels is of great benefit to migrating juvenile fish, the nitrogen supersaturation created by increased flow at the spillways causes enough mortality to pretty much cancel the benefit.

While barging the fish is not the natural solution it becomes the best way around the dams with increasing flows.

Studies have shown that the greatest survival of migrating juveniles comes with increased flow and natural migration to the collectors at the uppermost dam followed by barging and release at a point well below the supersaturated water from the lowest dam.

Perhaps a more natural solution might be found with creating more natural river flows in the future?
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Why are "wild fish" made of meat?