The Refuge contains both permanent and seasonal wetlands. Permanent wetlands are kept flooded year-round, while seasonal wetlands are drained, or "drawn down" in spring and summer to promote the germination of food plants needed by waterfowl. In the fall, these wetlands are re-flooded allowing ducks and geese to forage. Periodically, seasonal wetlands are disked to "recycle" old vegetation and increase their productivity. These shallow wetlands warm up early in the spring, producing large amounts of invertebrates which provide waterfowl with the protein necessary for egg production and food for their young.
In combination with cereal grains, seasonal wetlands provide habitat to support peak waterfowl populations of 10,000 birds, especially mallards, in the fall. Seasonal wetlands include the River Bed Unit, Greenhead, and Mallard marshes on the north end of the Refuge; and Heron, Teal, and South Ponds on the south end. Since the southern wetlands are interconnected, they lack independent water management necessary to produce optimal wetland habitat. Dam operations on the Kootenai River also negatively affect wetland management capabilities.
Permanent wetlands such as Center, New, Redhead, Waterline, Snipe, and Island Ponds, contain a moisture of relatively deep (6 inches to 4 feet) open water and dense stands of emergent plants (cattail and bulrush). These wetlands provide nesting habitat for waterfowl (e.g. redheads), rails, and black terns and attract tundra swans in fall and winter. Ideally, these wetlands should contain a 50:50 mix of emergent plants and open water. Periodic drawdowns and disking are used to reduce emergent cover and achieve this optimal mix.