Based on these remains, found in the same locality as Camarasaurus supremus, Cope determined the animal to have been smaller than the extant American Alligator and named the species A. lucasii after Superintendent Lucas who initially made the discovery.

The cranial material was examined by Charles C. Mook in 1942 who referred it to the type species not only on the basis of its locality, but also its matching size, general morphological characters and the absence of any other crocodilian remains from the area.

In 2012 Eric Randall Allen argued that the goniopholidids found in the Morrison Formation differ significantly from their European counterparts in the anatomy of the palate, with the choanae fully splitting the palatines unlike in the taxa from the UK and mainland Europe.

Furthermore, it is noted that there are no significant differences between A. lucasii and the only known material of A. gilmorei, with the only notable morphological character being artificially created by breakage, rendering it a junior synonym of the genus' type species.

This adaptation for semi-aquatic life would have allowed Amphicotylus and other Neosuchians to completely cut out the oral cavity from respiration, giving it the ability to open its mouth underwater while continuing to breathe as long as the nares are above the surface.