Spanish Army Lieutenant Gabriel Moraga was the first European to explore what is now the interior valley of California. His journey left an indelible mark on the state, giving Moraga the liberty of naming most major rivers and landmarks. He and his explorers were astonished upon first entering the valley. They noted the great wealth of wildlife that they could view for as far as the eye could see. Everywhere they looked there were ducks, geese, cranes, herons, pelicans, curlew, antelope, deer, elk and grizzly bears all living their lives undisturbed. Prior to their visit only the local Indians had ventured into the area.

On June 21, 1805, Moraga brought his Spanish Calvary from the Presidio of San Francisco and traversed over the Pacheco Pass. He was under orders from the Spanish Governor of California to explore the San Joaquin Valley. The pass would later become the principal route between the coastal areas to the west and the great valley and mountains to the east. During his journey, he gave the name "Modesto" to the area that is now home to the city of the same name. Moraga also discovered and named the Calaveras River after finding human skulls at it banks. The skulls were remnants of an ancient indian battle. "El Rio De Las Calaveras" means "The River Of Skulls".

In 1806, he lead his expedition to modern-day Kings Canyon, California and named "The River of the Holy Kings." Later it was shortened to "Kings River." During this part of his trip, he also named "Sacramento", which means "Blessed Sacrament". After discovering yet another major river in the central valley, Moraga named it after "Our Lady Of Guadalupe". It was later renamed to honor a native indian leader by the name of Estanislao . . the Stanislaus River. He also named the Merced River during this expedition, in honor of "Our Lady Of Mercy".

In 1808, Gabriel Moraga ventured in to the central valley from the coastal mission at San Jose to find more potential sites for new Spanish Missions and pursue indians that had fled from San Jose. According to written history, Moraga was the first non-native explorer to enter what is now the San Joaquin Valley.

During his trek, he named a small creek after Saint Joachim, who was the father of Mary, the Virgin mother of Jesus Christ. "Saint Joachim" translates, in Spanish, to "San Joaquin". It was later discovered that the creek fed in to a larger river, which then took on the same name. Being the major tributary through the valley, the name of the river soon propagated to the entire central Valley, becoming known as the San Joaquin Valley.

In 1850, California named the county that bordered the river as "San Joaquin County".