Measuring about 40 centimetres (16 in) long, Cartorhynchus was a small animal with a lizard-like body and a short torso; it probably swam in an eel-like manner at slow speeds.

The most distinctive features of Cartorhynchus were its short, constricted snout, and its multiple rows of molar-like teeth which grew on the inside surface of its jaw bones.

[4] Cartorhynchus had an unusually short and constricted snout, which only occupied half of the skull's length, and a deep jaw.

Due to its likewise elongated premaxilla, its bony nostrils were located relatively far back on the skull, and its frontal bone also lacked an expansion at its rear outer corner.

[1][6] Initially, Motani and colleagues inferred that Cartorhynchus was toothless; however, micro-CT scanning subsequently revealed the presence of rounded, molar-like teeth that projected inwards nearly perpendicularly to the long axis of the jaw, therefore making them invisible externally.

[1] Unlike Sclerocormus, the neural spines projecting from the top of the vertebrae in Cartorhynchus were relatively narrow and inclined instead of broad and flanged.

Cartorhynchus can also be distinguished by its parapophyses, vertebral processes that articulated with the ribs; their front margins were confluent with those of the vertebrae.

[6] Both Cartorhynchus and Sclerocormus had heavily-built ribcages, which were deepest near the shoulder, with broad, flattened, and thick-walled ribs, as is commonly seen in early members of secondarily-aquatic reptile lineages.

[10] On the underside of the chest, the gastralia of Cartorhynchus were thin and rod-like, unlike the flattened "basket" of Sclerocormus, but both lacked another pair of symmetrical elements at the midline of the body.

Notably, the close relation between these different groups was recovered by their analyses regardless of whether characteristics linked to aquatic adaptations were removed from the analysis.

[1][6] Such characteristics may have developed homoplasiously (from convergent evolution) among multiple lineages due to similar lifestyles, which can bias phylogenetic analyses to reconstruct them as homologies (derived from shared ancestry).

[13][14] However, the discovery of multiple diverse faunas of marine reptiles occurring in the Early Triassic — including Cartorhynchus — subsequently showed that this was not the case.

Huang and colleagues observed that the development of molariform teeth occurred independently many times in aquatic animals (including multiple lineages of monitor lizards, moray eels, and sparid and cichlid fish), and thus the frequency among ichthyosauriforms is not unusually high.

[21] Ichthyosauriforms did not recover in diversity after this turnover,[22] with the Sauropterygia and Saurosphargidae driving a second wave of diversification lasting three to five million years.

[26] They suggested that the jaw may have been twisted during preservation, or soft tissues like collagen which held up the teeth in life may have been lost, although they conceded that neither hypothesis would explain the wear patterns.

However, Motani and colleagues suggested in 2014 that it was still an adult because many early-diverging members of marine reptile lineages have poorly-ossified limbs through paedomorphosis (the retention of immature traits into adulthood), although they did not completely reject the possibility that it was a juvenile due to the existence of only one specimen.

[1] In the case of Cartorhynchus, Motani and colleagues proposed that the large, flipper-like forelimbs would have enabled it to move on land, thus making it amphibious.

Motani and colleagues suggested that other traits of Cartorhynchus would also have aided an amphibious lifestyle, including the short trunk and snout, and the thickened ribs (which would have served as a ballast, stabilizing the animal in near-shore waters).

However, Cartorhynchus would have likely swam at slower speeds requiring less efficiency, and the advantages of carangiform swimming in later, larger ichthyosauriforms were also offset by increased body size.

[31] Bed 633 of the Majiashan Quarry, the locality where Cartorhynchus was found, is a layer of grey argillaceous (clay-bearing) limestone located 13 metres (43 ft) above the base of the Upper Member of the Nanlinghu Formation.

[39][40] Potential invertebrate prey for Cartorhynchus include small ammonites and bivalves, and the thylacocephalan arthropod Ankitokazocaris.