It was founded in 1913 by a Russian group of settlers, members of the New Israel religious sect, who migrated under the influence of the then spiritual leader Vasily Lubkov, from the Voronezh region of Russia.

[2] On 1 July 1953, the status of San Javier was elevated to "Pueblo" (village) by the Act of Ley Nº 11.969.

In 1984, the town became known throughout Uruguay for the execution of Vladimir Roslik, a Russian-Uruguayan medical doctor who was tortured and later killed by the Uruguayan military.

Today the inhabitants of San Javier are proud to have maintained many of their traditions, including food, dances, embroidery and music.

Over the years, Russian marriages have been memorable events with three days of festivities that include dancing, singing, and traditional meals.

Tourism is not yet well developed in the park, however there is limited accommodation in San Javier, and a well-equipped camping area at nearby Puerto Viejo ('Old Port').