Its fossils have been found in northern South America, in rocks dating from the Middle Miocene to the very start of the Pliocene, about 13 to 5 million years ago.

Male specimens are known to have possessed bony horns growing from the front edges of the shell and the discovery of the fossil of a young adult shows that the carapace of these turtles flattens with age.

Stupendemys was first named in 1976 by Roger C. Wood based on specimen MCNC-244, the medial portion of a large sized carapace with associated left femur, scapulacoracoid and a cervical vertebra.

[2] In 2006 a second species, Stupendemys souzai was described by Bocquentin and Melo based on material from the Solimões Formation in Acre State in Brazil, also home to the giant Caninemys.

[3] In February 2020, Cadena and colleagues published a paper describing material discovered during the routine excavations in the Urumaco Formation, which have been ongoing since 1994.

The material includes a relatively complete carapace that set a new maximum size for the genus and was designated as the allotype, meaning the specimen is of the opposite sex of the holotype.

The nodular contours on the surface are irregular and the frontal margin of the shell is characterized by a deep notch flanked by large horns in male specimens.

The single most parsimonious tree resulting from the second analysis recovered Stupendemys as an early branching member of a clade with Peltocephalus dumerilianus at its base.

Despite their similar size (both sporting a carapace length greater than 2 meters), they vary greatly in skull morphology, with Caninemys proposed to have been deploying a vacuum feeding strategy combined with a strong bite supported by tooth-like structures of the maxilla, while a more durophagous-omnivorous diet has been suggested for Stupendemys.

In addition to the different skull morphology, the two taxa may have also been able to coexist due to the sheer size of the Pebas Mega-Wetlands they inhabited, as this ecosystem stretched over most of northern South America during the Middle Miocene.

Furthermore, Cadena and colleagues also highlight the role of turtles as seed-dispersers in modern-day Amazonia, consuming fruit of palms for example (Arecaceae), seasonally sometimes in great quantities, even if they are not typically part of their standard diet.

However other traditionally sexually dimorphic traits of the turtle shell, such as a deeper anal notch or a xiphiplastral concavity, have not yet been observed in Stupendemys fossils.

In addition to its small size, the animal is identified as a juvenile to young adult based on the absence of large horns and shallow anal notch.

With age the shell of the turtle grows significantly flatter, while the nuchal region develops a pronounced upturn of its anterior margin and peripheral 1, creating a wide and deep anteromedial embayment of the carapace.

The 2nd and 3rd vertebral scutes grow narrower as the animal matures from juvenile to adult, similar to the extant Podocnemis, Erymnochelys and Peltocephalus.

[5] During the Middle Miocene, the area inhabited by Stupendemys was part of an interconnected series of lakes, rivers, swamps and marshes that drained into the Caribbean known as the Pebas Mega-Wetlands, which included the Colombian La Victoria Formation.

[7] The Wetlands provided favorable conditions to the native reptilian fauna, with several lineages of crocodilians reaching enormous sizes during the Mid to Late Miocene and also diversifying in ecology.

[4] As the Pebas System began to disappear with the onset of the transcontinental Amazon Drainage, Stupendemys persisted in the wetlands of the northern Urumaco Formation and the Solimões Formation in Acre State, Brazil, into the Late Miocene before eventually dying out during the Early Pliocene like much of the large crocodilian fauna of the Miocene wetlands.