It was found in Late Paleocene-age rocks of Billings County, North Dakota, United States.

Wannaganosuchus is based on SMM P76.28.247, a mostly complete skull and postcranial skeleton missing some vertebrae, coracoids, part of the feet, ribs, and other pieces.

SMM P76.28.247 was found semi-articulated in the lower part of the Bullion Creek Formation, near the base of a lignitic clay layer deposited in a marsh setting on a floodplain.

[3] Wannaganosuchus was found in a layer with abundant plant fossils suggesting the presence of a swamp forest in the area; taxodioid logs are common.

[2] Recent studies have consistently resolved Wannaganosuchus as a member of Alligatorinae, although its relative placement is disputed, as shown by the cladograms below.