SF, you didn't direct your question to me, but I am familiar with salmon recovery issues in a couple of Puget Sound watersheds, and have a decent understanding of limiting factors for anadromous fish productivity in others. Based on the work that I have seen or been a part of, your hunch is correct. We've disconnected or outright destroyed large quantities of floodplain and tributary habitats in these watersheds. The various species use the habitats differently, but whether its floodplain connectivity that "absorbs" otherwise scouring flows, or direct juvenile rearing habitat, the loss of early emergence refuges and rearing space creates a freshwater habitat bottleneck that is limiting anadromous productivity. In some watersheds, you can add in the altered hydrograph due to increased impervious area and deforestation of headwaters, not to mention pollution, summertime water withdrawals, etc. etc. that exacerbate the problem.
Seriously though, that’s both encouraging, and disappointing to hear. Encouraging to hear what the root problems really are, and disappointing knowing they will be next to impossible to correct - at least to anything resembling the original state.