Kovalevski, who was born at Shustyanka, near Dvinsk (now Daugavpils in Latvia), took a science doctorate at the University of St. Petersburg, where he later taught and became professor (1891–93). He also taught at the universities of Kazan (1868–69), Kiev (1869–74), and Odessa (1874–90) and in 1890 he was elected to the Russian Academy of Sciences.

One of Kovalevski's most notable contributions to zoological science and the fuller understanding of evolution lay in his demonstration that all multicellular animals display a common pattern of physiological development. His research into the embryology of primitive chordates, such as Amphioxus (the lancelet), Balanoglossus (the acorn worm), and the sea squirts, particularly his demonstration of the links between them and the craniates, provided the basis for later studies of the evolutionary history of the vertebrates and led to Haeckel's theory that all multicellular animals are derived from a hypothetical ancestor with two cell layers. Kovalevski's most important publications are Development of Amphioxus lanceolatus (1865) and Anatomy and Development of Phoronis (1887).