Born in Mont-Roig del Camp in 1920, he moved to Barcelona in the 1930s when his father, a state school teacher, was posted to the capital. A man committed to freedom, Ballester volunteered at the age of 17 to defend the Spanish Republic against fascist aggression. He suffered the shameful refugee camps in the south of France until he was able to return to Barcelona. At the end of the Spanish civil war, he obtained a doctorate in Chemistry and Biological Sciences with an excellent cum laude mark for his doctoral thesis.

He was Professor of natural history in the University of Barcelona (1900) where he had problems due to his evolutionist ideas. In 1907, he founded and directed the Laboratorio de Biología Marina de las Baleares, in Mallorca, and the Instituto Español de Oceanografia. In 1939 he was exiled to Mexico.