Although Champsosaurus is well-known in Late Cretaceous and Paleocene deposits of North America, their cranial anatomy is poorly understood. Here, a well-preserved skull of Champsosaurus lindoei is described in detail using high-resolution micro-CT scanning. This confirms the presence of the putative neomorphic bone, which may be homologous with the pre-existing stapes, or developed through incomplete fusion of dermatocranial ossification centres. The ventral openings on the skull of Champsosaurus relate to the fenestrae ovales, an unusual configuration that may be convergent with other aquatic reptiles. Overall, the endocranial anatomy of Champsosaurus is typical for a basal diapsid. The morphology of the pars inferior of the inner ear suggests that Champsosaurus were capable of detecting sound underwater, and geometric morphometric analyses of the semicircular canals suggests that they were specialized for detecting head movements in an aquatic environment. Taken together, these results suggest that Champsosaurus were well adapted for an aquatic lifestyle.