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 24-40,000 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 plans (cattail and bulrush).  These wetlands provide nesting habitat for waterfowl (e.g. redheads), grebes, 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.

There is approximately 225 acres of riparian habitat (forest and shrubland along rivers and streams) on the Refuge.  Historically, riparian habitat covered extensive areas of the Kootenai River Valley.  Accounts described the valley as a maze of seasonally flooded forests and backwaters.  Riparian areas provide important habitat for resident and migratory birds, supporting more species than any other habitat type; and by providing shade, keep streams cool for native fish.  

About 532 acres of forest occurs on the refuge and is second growth timber as evidenced by stumps and partially brushed in roads.  However, some stands on the refuge are old enough (about 100 years) to have developed distinct old-growth characteristics.  Slopes are steep, exceeding 30% in many places.  The "corduroy" terrain creates a series of aspects that vary from relatively dry, open areas with Ponderosa Pine, to colder, wetter sites dominated by Western Red Cedar.  Douglas Fir is the most common species on the dry and moist sites.  Other conifers include grand fir, western larch, and western hemlock.  Large cottonwoods are found along streams in lower elevations, along with some aspen and birch.

The refuge manages grasslands for foraging elk, deer, and to a lesser extent moose as wells as areas for ground nesting birds. Grasslands in the closed area of the refuge are seeded to various pasture mixes and maintained through mowing and control of noxious weed species. These grasslands are an extremely important winter food source for as many as 240 elk and 80 deer.

During the establishment of the refuge, neighbors were concerned that waterfowl would feed on their crops as the refuge increased the waterfowl population.  The Fish and Wildlife Service (FWS) assured farmers that crops would be grown on the Refuge to provide feed for waterfowl and reduce the severity of crop depredation on their private land.  Planting grain to "accommodate waterfowl" and "lessen the threat of depredation locally and elsewhere" was stipulated in the Kootenai National Wildlife Refuge Master Plan in 1965.  During its early years, a total of 1,876 refuge acres were farmed, hayed, or grazed.  As wetlands were developed, haying and grazing were eliminated and farming was reduced to approximately 600 acres.  Two former landowners of refuge property stayed on as cooperator farmers until 1995.  Cooperators harvested 60% of the crops and in return left 40% standing for waterfowl food.  In 1997, the cooperative farming program was phased out and converted to farming using only Service staff and equipment.  The purpose of this shift from cooperative farmers to Service staff was to produce about the same amount of crops, but reduce the overall footprint of agricultural lands in order to restore more wetlands for waterfowl.

Grain continues to be an important food source for migrating waterfowl.  Today approximately 470 acres of cropland is managed for waterfowl, and of that, 160 acres are plowed and seeded to winter wheat, barley, and millet every year on a rotational basis.  While volunteer crops in the unseeded acres reduce the cost of annual planting, they require more weed control.

The portion of Deep Creek on the refuge is primarily a migratory cooridor for rainbow, cutthroat, and bull trought to more suitable habitat higher in the watershed.  The incised channel that has formed due to various land uses and backwater from the Kootenai River makes restoration quite challenging.

Myrtle Creek exceeds the Clean Water Act's standard for water temperature.  Bull trout, a threatened species, have been observed on numerous occasions over the last 10 years, but only the upper 400-600 meters of the Creek can be considered suitable habitat.  Over the years, efforts to plant trees and shrubs along the Creek to increase shading, reduce the water temperature, and improve wildlife habitat proved unsuccessful due to the altered hydrology of the Kootenai River.  In 1997, the Kootenai Tribe of Idhao, in cooperation with the Idaho Fish and Game, the U.S. Fish and Wildilfe Service, adn the BC Ministry of Environment, Land, and Parks, began a kokanee reintroduction program in the westside tribuatries of the Kootenai River.  Kokanee eggs were introduced in man-made redds (gravel nests) in Myrtle Creek in teh fall of 2003, 2004, 2005, and 2007.  In September 2008, kokanee were observed spawning in the Creek.