The fossils of Baptornis advenus, the type species, were discovered in Kansas, which at its time was mostly covered by the Western Interior Seaway, a shallow shelf sea.

More material evidence exists for the ecology of B. advenus than for any other member of the Hesperornithes, with the possible exception of Hesperornis regalis, but still much is left to conjecture.

Presumably, it thus behaved in a manner similar to today's darters, hunting smaller, more mobile prey than its larger relatives.

While it was excellently adapted to swimming and diving, Baptornis is thought to have been clumsy on land, pushing itself along the rocks with its feet rather than actually walking.

The natural position of the lower legs was flush against the body, with the feet stretched out sideways and thus it would have been unable to move upright without toppling over.

As opposed to Hesperornis which almost certainly had to slide on its belly or galumph like an earless seal, Baptornis's lower leg was not as firmly placed along the body sides.

Baptornis had powerful gastric juices and/or regurgitated most indigestible parts of its prey as a pellet like most living fish-eating birds do, because the Enchodus remains make up only a small fraction of the coprolites' mass, most of which was nondescript feces.

[4] In addition, two other prehistoric diving birds of the Late Cretaceous are sometimes placed in the Baptornithidae: Potamornis is in all probability a member of the Hesperornithes.