From its primary source on the Paraná River, about  south of Reconquista, the San Javier flows generally south, parallel to the Paraná. It passes by San Javier and Helvecia. Its mouth does not discharge directly into the Paraná River but rather into several channels near Santa Rosa de Calchines.
The San Javier River originates from its primary source on the Paraná River, south of Reconquista, flowing generally southward parallel to the Paraná River, passing through San Javier and Helvecia before emptying into several channels near Santa Rosa de Calchines.