The Army Corps of Engineers says its policy prohibits trees on most levees because trees can cause structural damage. The roots can create holes allowing water to move through, and if a tree is blown over it often takes a chunk of the levee with it.
But the trees on the targeted levees provide crucial riverside habitat for endangered species says Jordan Traverso of the California Department of Fish and Game.
TRAVERSO: "Most of them are Central Valley levees, that have original riparian forest habitat. There's only about 5 percent of that original riparian forest left, and it houses a lot of endangered species."
Threatened species includes the Chinook salmon, Central Valley Steelhead and Swainson's hawk.
Part of the lawsuit hinges on a procedural technicality in the Endangered Species Act. The Department of Fish and Game says the Army Corps failed to complete the environmental documents required before a policy change.
The Corps maintains that their policy is not new, and it's been around for decades with only minor changes.