The outpost was informally known by that name, meaning "boat" due to its strategic location north of the confluence of the Bermejo and San Francisco Rivers.

The site later belonged to Celedonia Reyes de Prado, who sold the land to a partnership between the Leach brothers and Dr. Carlos Serrey on July 12, 1909.

Adopting San Roque as the town's patron saint, Embarcación had a hospital inaugurated in his honor in 1938, and the Catholic Parish, built in the 1960s, is so named as well.

Salvita, a local fruit and vegetable packaging and distribution firm, was established by Salvador Muñoz, and is the leading buyer for the area's growers.

The largely agrarian town, where 70% of residents lived in substandard housing at the 2001 census, embarked on a significant public works agenda in 2010.