At age thirteen, Fontana entered the Military Command of Río Negro as a trainee; he later fought in the Paraguayan War.

After the war ended, he lived for a time in Buenos Aires, where he studied natural sciences, astronomy, and physics under Hermann Burmeister.

During one expedition, he lost his left arm in a violent encounter with an indigenous group in the region.

There he directed the expedition to the west with an exploratory group named the Chubut Riflement (Rifleros del Chubut), which discovered the October 16 Valley (Valle 16 de Octubre), a fertile area in the foothills that would later be the site of the Welsh colony of Trevelin.

Fontana spent his later years in San Juan, where he held various public and community offices.