Chase Lake itself comprises 2,503 acres with the remaining refuge acreage consisting of native and tame grasslands and small wetlands. The topography is steep to rolling with the lake being the lowest point on the refuge.
Chase Lake has no outlet, is highly alkaline and supports no aquatic vertebrate life.
The two islands in the lake are home to the refuge's primary attraction, its thousands of nesting white pelicans, gulls, and cormorants. The white pelican breeding colony at Chase Lake numbers between 10,000 and 12,000 birds and is the largest colony in North America. Chase Lake NWR was declared a wilderness area in 1975. The entire refuge except for 230 acres southwest of a Bureau of Reclamation power line is included in the wilderness area. The refuge is managed by the use of prescribed burning.