Anhanguera was a fish-eating animal with a wingspan of about 4.5 m (15 ft). Like many other ornithocheirids, Anhanguera had a rounded crests at front of its upper and lower jaws, which were filled with angled, conical but curved teeth of various sizes and orientations. Like many of its relatives, the jaws were tapered in width, but expanded into a broad, spoon-shaped rosette at the tip. It is distinguished from its relatives by subtle differences in the crest and teeth: unlike its close relatives Coloborhynchus and Ornithocheirus, the crest on the upper jaw of Anhanguera did not begin at the tip of the snout, but was set farther back on the skull. Like many ornithocheiroids, (most notably the pteranodonts but also in ornithocheirids such as Ludodactylus) Anhanguera had an additional crest protruding from the back of the skull. However, it was reduced to a small, blunt projection in these animals.
A study in 2003 showed that Anhanguera held its head at an angle to the ground due to its inner ear structure, which helped the animal detect its balance.