Herds of elk live in the monument and surrounding areas.

With over 40 million years of fossilized history related to the evolution of mammals in the region, it would be fun to come to the John Day Fossil Beds to see an entelodont (pig and hippo relative), diceratherium (rhino relative), miohippus (horse relative), brontothere (thunder beast) or pogonodon (John Day tiger) still roaming the hillsides.

However, the shrill bugle of a bull elk on a cool September evening can bring a similar thrill to the visitor (except for maybe a hardcore paleontologist).

Seeing the tracks of a cougar that has crossed a hiking trail, or hearing the excited yips of a successful coyote pack on a hunt can bring a similar feeling. With the John Day River, Rock Creek, and Bridge Creek flowing through the monument's boundaries, the chance to see the mammals tied to these lifelines are varied and many.

Gophers and ground squirrels thrive around the 3 units of the monument, making it possible to see the frenzied digging of a badger in pursuit of a meal. Sitting quietly along the John Day River may be rewarded by the sighting of a beaver or river otter swimming by or a mink or raccoon hunting along the bank. Deer forage in the fields and along the ridges with an occasional sighting of a "monster" buck in their midst.

During the summer evening hours, bats commonly leave their roosts in the buildings, cracks, and caves to feed on insects overhead. The hay meadows and grass & sagebrush covered hills support thriving populations of voles, mice, shrews and rabbits which are a major prey base for the many predators in the area. And scattered through the geologic cracks and caves of the monument are homes of the bushy-tailed woodrat with their middens (food stashes) for the coming winter.