The slow flowing Columbia River meanders between natural levees for the first 100 kilometres of its length, maintaining an extensive and complex network of shallow ponds and oxbows behind its levees. The units of the Columbia National Wildlife Area are located in that stretch of valley bottom wetlands.
Vegetation is a transition between wet interior forests to the north, and dry forests to the south.
It is located in that stretch of the river valley that is surrounded by the Dry Forest Biotic Area characterized by yellow pine, black hawthorn, choke cherry, serviceberry, and mock orange on the benchlands, and Douglas fir and western larch at higher elevations. On the river banks and levees black cottonwood, trembling aspen, black poplar, and paper birch are found. On wetter sites willows, bog birch, and sedges abound. Emergent vegetation of the marshes includes cattail, bulrush, and horsetail, submergents include yellow pond-lily, pondweed, and stoneworts. The Rocky Mountain Trench is an important migration corridor for birds in the Pacific Flyway.