About 80 percent of the refuge is located in the Sutter Bypass, a floodwater bypass from the Sacramento River that floods at least once a year and may cover portions of the refuge with up to 12 feet of water. Sutter Refuge typically supports wintering populations of more than 175,000 ducks and 50,000 geese.

The mixed riparian forest habitat on the refuge is important for breeding and migrating passerine birds, and supports a large heron/egret rookery. The refuge provides habitat for several Federal and State endangered and threatened species, including giant garter snake, winter-run Chinook salmon, yellow-billed cuckoo, and Swainsons hawk.

Water manipulations are used to encourage or discourage vegetation species, create suitable depths for a variety of wildlife, and minimize mosquito production. Since levee systems on local rivers prevent natural flooding, most refuge wetlands are largely "artificial."

Water is delivered through local irrigation districts. Significant quantities of mixed riparian forest occur along the perimeter of the refuge, forming habitat for many land bird species and other wildlife. The refuge's annual habitat management plan sets objectives and directs management activities, prioritizing work on approximately 20 habitat units.

The plan includes floodup and drawdown dates, vegetation manipulation required, levee repairs, special management considerations, and other tasks required to meet refuge objectives. Standardized ground and aerial wildlife surveys and vegetation surveys are conducted regularly throughout the year to inventory populations and document habitat use.

Each year units are evaluated by how well they met habitat and wildlife use objectives. The manager, biologist, and field crew revisit each unit annually, using the wildlife and habitat data to assess the previous year and to formulate the upcoming year's plan. Management of exotic or rank vegetation is accomplished with various combinations of burning, grazing, herbiciding, and water management.

Data on these efforts are stored in a computer database where they can be accessed, analyzed, and reported. Research is encouraged, and staff members are involved with initiating and conducting studies that have direct applications to management.

The United States Congress designated the Three Arch Rocks Wilderness in 1970 and it now has a total of 15 acres. The Three Arch Rocks NWR, part of which is designated as the Three Arch Rocks Wilderness, is closed to visitation to protect wildlife and other natural, cultural, and/or other resources consistent with the conservation purpose(s) of the refuge.