Judge James Redden of Federal District Court in Portland ruled Tuesday that the plan, known as a biological opinion, is too vague and uncertain on specific steps that will be taken in future years to improve salmon habitat.
He added that he did not think the government could meet the standards of the Endangered Species Act by habitat improvements alone, and that it was time to consider new options, including removing some of the dams.
The judge left the plan in place through 2013, when federal agencies must come up with more specific projects to help salmon.