He studied medicine at the Universities of Heidelberg, Würzburg and Giessen, earning his doctorate at the latter institution in 1829. Afterwards he settled in Frankfurt am Main, where he worked as a general practitioner of medicine while maintaining an active interest in botany.
As a student in Heidelberg and afterwards, he studied botany with his friend George Engelmann (1809-1884), who later became a renowned German-American botanist. From 1831 Fresenius was curator of the Senckenberg herbarium and a teacher at the Senckenberg Research Institute (Forschungsinstitut Senckenberg). With his student Anton de Bary (1831–1888), he conducted microscopic investigations of algae and fungi. He died in Frankfurt on 1 December 1866 at the age of 58.
The plant genus Fresenia from the family Asteraceae is named after him.
- Grundriss der Botanik, zum Gebrauche bei seinen Vorlesungen, 1840 - Outline of botany, etc.
- Beiträge zur mykologie, 1850 - Contributions to mycology.
- Beiträge zur Kenntniss mikroskopischer Organismen, 1856 - Contributions to the understanding of microscopic organisms.
- Cordiaceae, Heliotropieae, Borragineae, 1857 - Cordiaceae, Heliotropioideae, Boraginaceae.