As part of the Great Salt Lake ecosystem, the Refuge now hosts the largest colony of White-faced ibis in North America. The wet meadows and mudflats on and surrounding the Refuge are excellent feeding habitat and bring the ibis in from April through October, and the deep emergent marshes provide nesting habitat for the colony throughout the summer.

While the Refuge is mainly used for foraging, the greater Great Salt Lake ecosystem colony of American white pelican is one of the three largest North America. But the proximity of the excellent fishing on Refuge wetlands to the pelican colony is not to be discounted.

The remote and undisturbed drying mudflats, near water sources, are excellent feeding habitat for the diminutive Snowy Plover. The Refuge and the Great Salt Lake ecosystem host over 50% of the North American population.

While the Refuge hosts only 2-3% of the continental breeding population of Black-necked stilt, nearly 80% of the migrating population uses the Refuge and Great Salt Lake wetlands as an important stopover site.

Northern Utah's wetlands, including the Refuge, host up to 60% of the continental breeding population of Cinnamon teal. The Refuge wetlands and neighboring fine-structured grasslands provide necessary feeding and nesting habitat.

The deeper waters along the northwest boundary of the Refuge and neighboring Bear River Club provide important stopover feeding habitat for flocks of migrating Tundra swan.  These flocks, sometimes in numbering upwards of 60,000, find the sago pondweed, a submerged aquatic plant, nearly irresistable.