Opponents claim Caltrans has not done the proper environmental reviews and isn't doing enough to restore the damage the construction has caused.
The $300 million project is being built through federally protected wetlands.
Environmentalists have staged a number of protests, trying to shut down the bypass, which they say is unneeded.
Construction on the project continued while the two sides took the matter to court. Late Thursday, a judge threw out a lawsuit attempting to stop the project.
