The topography of the site is that of a badland, due to the downcutting of the Little Missouri River. The rock units are likely sediments derived from the Laramide orogeny deposited in an ecosystem dominated by rivers, streams, ponds, lakes, and swamps. The Wannagan Site is found in the upper portion of the Tongue River Formation. The rocks of this deposit, reaching a thickness of over 60 m, consist of yellow to tan, poorly lithified claystones, mudstones, and siltstones with a lesser amounts of interbedded fine-grained sandstones and lignite. The site is overlain by the Sentinel Butte Formation. This formation is generally gray to brown in color but is similar in lithology to the Tongue River. The Sentinel Butte is roughly 90 m thick. The between the two formations is roughly 6 m above the site. The Sentinel Butte contains an extensive stump-bearing petrified wood bed above the contact at the site.
Fauna
Many mammals are found at Wannagan. All are small compared to modern mammals, the largest being sheep-sized. Preserved mammals include a squirrel-like primitive primate and Ptilodus, an arborealmultituberculate. The largest mammal at the site is the condylarth herbivore Phenacodus. An additional mammal fossil is Protictis, a weasel sized member of Viverridae that may have hunted on the forest floor. Reptiles are the dominant animal type preserved at Wannagan. The largest animal found at the site is the eusuchian crocodilian Borealosuchus formidabilis. B. formidabilis is also thought to be the apex predator of the fauna. The second largest reptile is the champsosaurChampsosaurus gigas. C. gigas is unusual among Paleocene reptiles in that it is larger than its known Mesozoic ancestors: 3 meters in length versus 1.5 meters for the largest Cretaceous champsosaurs. Reptiles as a whole decreased in size after the Cretaceous–Paleogene extinction event. Other reptiles include soft-shelled turtles, varanid lizards, a small alligatorid called Wannaganosuchus, palaeophid snakes, and the snapping turtle-like Protochelydra zangerli. Birds from Wannagan include an ibis, an unnamed water bird, and a plover-like shore bird. The two types amphibians found at Wannagan are the giant salamanderPiceorpeton willwoodense and frogs. Fish include fossil Esox, freshwater rays, gar, and bowfin. Additionally, the dragonflyGomphaeschna schrankii and the mayflyEphemeropteran have been found.