Waagen was born in Munich, the son of a Prussian councillor and his wife, Nanette (née Schechner), who had been a singer.

[2] He received a Doctor of Philosophy degree at the University of Munich under Albert Oppel where he studied the rocks and fossils of the Jurassic system, and published an elaborate work on geology (Versuch einer Allgemeinen Classification der Schichten des oberen Jura)[3] that was crowned by the university.

Waagen's main work in British India was on the Jurassic cephalopods of Kutch and on the Salt Range fossils, both forming parts of the “Paleontologica Indica” and the latter was incomplete at the time of his death.

[6] In 1869, after an exhaustive study of ammonites, Waagen advocated the theory of orthogenetic evolution or mutation for certain series of fossils.

[7][8] As a young man he had taken an active part in the Catholic life of Munich, and two years before his death he wrote a treatise on the first chapter of Genesis that showed both the geologist and the Christian.

Waagen's most important works were: He wrote in English: "Jurassic Fauna of Kutch" (1873-6); "Productus Limestone" (1879–91); "Fossils from the Ceratite Formation" (1892).