Pterodaustro has a very elongated skull, up to 29 centimetres long. The portion in front of the eye sockets comprises 85% of skull length. The long snout and lower jaws curve strongly upwards; the tangent at the point of the snout is perpendicular to that of the jaw joint. Pterodaustro has about a thousand bristle-like modified teeth in its lower jaws that might have been used to strain crustaceans, plankton, algae, and other small creatures from the water. These teeth stand for the most part not in separate alveoli but in two long grooves parallel to the edges of the jaw. They have a length of three centimetres and are oval in cross-section, with a width of just 0.2 - 0.3 millimetres. At first it was suspected these structures were not true teeth at all, but later research established they were built like normal teeth, including enamel, dentine and a pulpa. Despite being made of very hard material, they might still have been flexible to some extent due to their extreme length-width ratio, a bend of up to 45° being possible. The upper jaws also carried teeth, but these were very small with a flat conical base and a spatula-formed crown. These teeth also do not have separate tooth sockets but were apparently held by ligaments in a special tooth pad, that was also covered with small ossicles, or bone plates. The back of the skull was also rather elongated and in a low position; there are some indications for a low parietal crest.
Pterodaustro had an adult wingspan of approximately 250 centimetres (8.20 ft). Its hindlimbs are rather robust and its feet large. Its tail is uniquely elongated for a pterodactyloid, containing 22 caudal vertebrae, whereas other members of this group have at most sixteen.
Pterodaustro probably waded in shallow water like flamingos, straining food with its tooth comb, a method called "filter feeding". Once it caught its food, Pterodaustro probably mashed it with the small, globular teeth present in its upper jaw. Robert Bakker incorrectly suggested that, like flamingos, this pterosaur's diet may have resulted in a pink hue. However, recent studies show that only Neoaves can sequester carotenoids for use as a pigment in the feathers rather than just the skin or beak, and even then they require to enhance it with structural colors, so a pink hue for any pterosaur seems extremely unlikely.
At least two specimens of Pterodaustro have been found, MIC V263 and MIC V243, with gizzard stones in the stomach cavity, the first ever reported for any pterosaur. These clusters of small stones with angled edges support the idea that Pterodaustro ate mainly small, hard-shelled aquatic crustaceans using filter-feeding. Such invertebrates are abundant in the sediment of the fossil site
A study of the growth stages of Pterodaustro concluded that juveniles grew relatively fast in their first two years, attaining about half of the adult size. Then they reached sexual maturity, growing at a slower rate for four to five years until there was a determinate growth stop.
In 2004 a Pterodaustro embryo in an egg was reported, specimen MHIN-UNSL-GEO-V246. The egg was elongated, six centimetres long and 22 millimetres across and its mainly flexible shell was covered with a thin layer, 0.3 mm thick, of calcite. Three-dimensionally preserved eggs were reported in 2014.
Comparisons between the scleral rings of Pterodaustro and modern birds and reptiles suggest that it may have been nocturnal, and may have had similar activity patterns to modern anseriform birds that feed at night.