Born at Trassilico, near Modena in Italy, Vallisneri studied medicine at Bologna under Marcello Malpighi and at Reggio where he obtained his MD in 1684. After practicing medicine in Reggio, Vallisneri was appointed to the chair of medicine at the University of Padua in 1700 where he remained until his death.

Francesco Redi in 1668 had performed a famous experiment proving that the maggots in rotten meat were not spontaneously generated but arose, in the normal manner, from eggs laid by flies. He did however spoil the force of his argument by conceding that the larvae found in galls, for which he could find no eggs, were spontaneously generated. In 1700 Vallisneri plugged this gap in his Sopra la curiosa origine di molti insetti (On the Strange Origin of Many Insects) in which he reported detecting eggs of the insects in plant galls.

In 1715 Vallisneri published Origine delle fontane (Origin of Fountains), which threw much light on another longstanding problem. Many ancient and medieval authorities were convinced that springs and rivers originated in the sea, and consequently the source of artesian wells, such as those at Modena, presented a problem. By exploring the local mountains, Vallisneri found that the rain and melting snow ran into fissures and formed subterranean rivers. Such rivers, passing under Modena at high pressure, would readily produce ‘fontane’ if deep enough shafts were sunk.

As a biologist and anatomist Vallisneri also produced a number of treatises on such unfamiliar animals as the ostrich (1712) and the chameleon (1715). His studies of a group of aquatic plants led to the genus Vallisneria being named for him.