Carl H. Apstein qualified as a zoologist through studies at the universities of Leipzig, Freiburg im Breisgau, and Kiel, obtaining the degree Doctor of Philosophy at Kiel in 1889 with a dissertation on the spinnerets of the orb-weaver spider. Subsequently he worked as assistant at the Zoologische Institut of the University of Kiel, initially concentrating on the study of the freshwater plankton of the lakes of Holstein. During his nine years at the institute he published about 15 papers (in German), some of them on spiders and marine invertebrates. In 1898 he was appointed lecturer in zoology at the University of Kiel, and was promoted to associate professor in 1906.
During 1898-1899 Apstein was a member of the German deep-sea expedition on the Valdivia, which visited the Cape in November 1898. From 6 to 12 November he collected marine algae and a few flowering plants around Cape Town. The expedition also visited the Kerguelen Islands, the Seychelles, and Sumatra. During 1903-1905 he took part in another expedition to southern Africa, which resulted in a paper by him on "Das Plankton der Kueste von Suedwestafrika". This paper was later published in Schultze, L. (1928), Zoologische und anthropologische Ergebnisse einer Forschungsreise im westlichen und zentralen Suedafrika ausgefuehrt in den Jahren 1903-1905. Fuenfter Band: Systematik, Tiergeographie und Anthropologie. Denkschriften der Medizinisch-Naturwissenschaftlichen Gesellschaft zu Jena, XVII, pp. 33-46.
From 1902 to 1911, in addition to his teaching post, Apstein worked at the Laboratorium fuer Internationale Meeresforschung. For many years he furthermore participated in research for the Seefischereiverein. His publications included Das Suesswasser-Plankton (Kiel, 1896), Tierleben der Hochsee (Kiel, 1905), and many additional papers on algae, plankton, fish, marine invertebrates, and zoological nomenclature. Several of his papers reported his studies of material collected during the Plankton Expedition of the Humbolt Foundation (1900), and the German South Polar Expedition of 1901-1903. In 1911 he joined the Akademie der Wissenschaften in Berlin as editor of zoological publications. From 1918 to 1945 he served as secretary of the Deutschen Zoologische Gesellschaft and for some time was a member of the International Commission on Zoological Nomenclature.