Laying at an elevation of 4,365 feet, the refuge is situated near the confluence of the north and south forks of the Pit River. Modoc NWR lies just beyond the western edge of the Great Basin, with the Warner Mountain range on the east and the Adin Mountain range on the west. Several habitat types are represented: freshwater lakes and wetlands, farmland and irrigated meadows, sagebrush upland and riparian corridors. In addition to the migratory bird populations, these diverse habitats support a wide range of other wildlife.  

Depending upon the season, bird populations vary greatly in abundance and diversity. Large concentrations of waterfowl visit the refuge during spring and fall migrations - a portion of these remain throughout the breeding season. A total of 246 bird species have been observed on the refuge, including 40 accidentals. At least 76 species have been documented as nesting at Modoc with another 18 species possibly nesting. 

Most mammals found on the refuge and adjacent land are resident species, except bats which are migratory. Visibility of mammals varies seasonally because some species hibernate in winter, and others, although active, remain out of sight in tunnels under the snow. Mule deer, however, are plentiful in the area and can be seen from refuge roadways. 

A variety of reptiles and amphibians can be found on the refuge, most often in or adjacent to wetlands or ponds, or sun bathing on refuge roads. Fish are found in nearly all irrigation channels, as well as the Pit river, pine creek, and Dorris Reservoir. Here is a list of Amphibians, Reptiles, and fish that can be found at Modoc NWR.