The groups want the river to flow more naturally, with a spring rise and shallow summer levels to ensure survival of endangered and threatened fish and birds.
The United States Fish and Wildlife Service ordered those changes in 2000, but the corps resisted. The service changed course last month, issuing a revised biological opinion calling for more modest flow changes that angered those on all sides of the issue.
A lawyer for the conservation groups called the new opinion a cookbook and said that following the recipe will lead to conflict.
Attorney David Hayes said that without explicit standards for determining river flows each year, there is no end in sight to the crossfire of lawsuits up and down the river.
Corps spokesman Paul Johnston said the agency's job is to follow the Fish and Wildlife Service opinion, not to question its validity.