The San Jorge was found by the Spanish conquistador Alonso de Heredia, while seeking to establish contact with the indigenous Zenú culture in the 1530s.

At that time the river was known under the name of Xegú or Jegu and its banks flourished numerous villages of pre-Columbian society as Yape Zenú (now Ayapel, Córdoba) and Tacasuán (now San Benito Abad).

In 1966 an American aviator sighted an extensive network of canals and artificial ridges along the San Jorge, finding that the "raking" was not natural but a work of human engineering.

In 1986, the Colombian archaeologists Clemencia Plazas and Anna Maria Falchetti, defending this thesis, showed that the ridges and channels built on the banks of San Jorge (covering about 50,000 square kilometres (19,000 sq mi) and are the largest of the river networks of Hispanic America) were the work of the pre-Columbian Zenú society, and that the San Jorge Valley was inhabited by a highly technological society can be seen as pottery and jewelry found on the banks of the river.

As this is an area that remains flooded for several months a year, it was necessary to create a drainage system to allow the permanent establishment of the population there.