He was the Ghosh Professor of Botany (1920–47) at the University of Calcutta; and Founder Director (1946–60) of Maharashtra Association for the Cultivation of Science.
He explored biodiversity of Western Ghats where he came across a species of freshwater jellyfish, which was until then only known to be found in Africa.
Dr. Annandale, the Superintendent of the Indian Museum in Kolkata, helped Dr. Agharkar in his further endeavours to collect, preserve and conduct microscopic examinations of animal and plant specimens.
Since childhood he was fascinated by plants and animals which led him to discover a new species of jellyfish.
He went to Germany to obtain the PhD degree from the University of Berlin in 1919 but was imprisoned as the World War I broke out.