U.S. District Judge Oliver Wanger says guidelines meant to protect the fish are unlawful.
Wanger does not dispute the pumps used to deliver water to valley farms and cities have harmed the threatened fish.
But he says parts of the 2008 Biological Opinion need to be rewritten to better determine how the pumping restrictions are impacting the valley's economy.
Tuesday's ruling is not expected to have any immediate impact on local water deliveries.
