Schmarda was born at Olmütz where he attended the Grammar School and the Philosophical Course at the University of Olomouc. He graduated in 1841. He studied medicine and science at the Josephinum, now part of the Medical University of Vienna , particularly interested in zoology, graduating in 1843 as "Dr Med et Chir.", as well as Magister of Ophthalmology and Gynecology. 
In 1843 he was appointed Chief Field Physician to the dragoon regiment, a mounted infantry ("Dragonerregiment"), and at the same time acted as assistant to "special natural history" at the Josephsakademie. During two scientific journeys to the Adriatic Sea, in 1844 and 1846, he made collections of marine life. In 1848, he became a teacher of natural history and geography at the secondary school in Graz. In 1848/49 he lectured at Joanneum on anthropology as a science and represented the School of Agriculture in 1848 and 1850.
From 1853-1857 he traveled around the world and in 1862 he was appointed professor at the University of Vienna. For the government he investigated the industry of fisheries on the Austrian (1863-1865)[dubious ] and French (1868) coasts. In 1883 he retired from service, and visited Spain and the African coast in 1884, 1886, and 1887.
Schmarda is credited with being the first scientist to have published the observation that microorganisms respond to light, which is considered the foundation for the development of ultraviolet germicidal irradiation.