It negatively affects the entire ecosystem. Salmon are just one of the species affected but are the most publicly visible.
The irony here is that striped bass are also in decline along with the rest of the ecosystem. This particular issue is just another smoke screen, of many, put in place by corporate agriculture and the DWR lawyers to divert attention away from the real issue of over pumping.

These two paragraphs from Joe's link sum it up pretty good.

Population growth and over expansion of agriculture put more water demands on the Delta than it could withstand and still remain a viable estuary. The ecosystem collapsed and thousands of aquatic species including salmon collapsed along with it.

Our primary adversaries in these water wars are the agricultural water contractors of the San Joaquin Valley. They want control of more of the public’s water and they could care less about fish. They have filed 13 lawsuits trying to overturn the biological opinions. They have also introduced six bills in congress trying to do the same thing. They are spending millions in a PR campaign against the fish. Money and control are bigger issues than watering crops. When they get allocations of subsidized water, many of them are selling it instead of growing crops. By selling it they make up to ten times their cost. The U.S. Bureau of Reclamation and the California Department of Water Resources (DWR) support the water contractors and oppose most salmon recovery projects. DWR is leading the lawsuits to overturn the biological opinions.


MT