Portable and permanent pumps will be used to raise and lower the water levels in the new pools, essential to sustain aquatic plant growth. The dikes will offer added wildlife observation opportunities to visitors on foot. Maintaining existing quality marshes Limiting woody vegetation encroachment into marshes Refuge manager Rick Frietsche expects greater numbers of shorebirds than ever before when he can create mudflats with the refuge's new water control system. Habitat damage from the large population led to a hunting program for antlerless deer that has reduced the herd to a size supported by the habitat. Other management controls in use at the refuge are prescribed fires and insect releases to limit the growth of exotic leafy spurge and purple loosestrife.
Predominate fish are black and brown bullheads.
Refuge waters are open to public fishing, although selected sections are closed to avoid wildlife disturbance. By far the greatest public use of Trempealeau NWR is for wildlife observation. Visitors are greeted with a 5 mile auto tour route that includes an observation deck affording superb views of wildlife on one of the refuge's new pools. Recent sightings from the deck were 138 eagles on one day and a great horned owl nest in a nearby tree. Labels on another 1 mile trail identify the grasses and forbs that are found in the restored prairie.