The church is located at the foot of a mountain, unlike other Sarov churches and the monastery, and stands on a high arched foundation. This is explained by the fact that it was built directly over a spring that once flowed from under the mountain and gave rise to a stream that flowed into the Satis River. Near this spring, the first monk buildings appeared, and their settlement later became the Sarov Desert. Initially, the builder John planned to erect the first church of the Sarov Desert right here, but later changed his decision. Therefore, the church is unofficially called the temple over the well of the Originator.

The construction of the stone church in honor of John the Baptist over the spring began under builder Philaret from 1747 to 1749, continued under Markell from 1749 to 1751, and was completed with the consecration on September 13, 1752. The church was small, with one altar and one dome. The name of the church over the spring was explained by A. N. Muravyov as follows: "it is quite appropriate that it is dedicated to the Baptist, over the waters, on which the Jordanian consecration is performed."

In 1812, a stone staircase was built leading down to the church along a steep slope. It was constructed by a team of stone masons from Temnikov under the guidance of merchant Andrei Martynovich Sitnikov and townsman Ivan Alexeyevich Telyatnikov.

The church in its original form stood for about 70 years. In 1820, Sarov was visited by Astrakhan fish industry worker Collegiate Assessor Kirill Fedorovich Fedorov, who wished to donate funds for the expansion of the church. In 1821, the old church was dismantled, and construction of a new one began. The work was completed in 1824, during which Fedorov donated 30,580 rubles, and another 10,000 rubles were given for the maintenance of the church.

At Fedorov's request, the church was made three-altar: the main altar was dedicated to John the Baptist, and two additional ones to the Apostle James the Less and Cyril of Jerusalem, saints of the donor's birthday and name day.

The main altar was consecrated by Bishop Athanasius Telyatev of Tambov on June 19, 1827. The left altar, in honor of James the Less, was consecrated by the rector Niphont on September 30, 1828, and the right altar by Bishop Arsenius Moskvyn of Tambov on July 1, 1834. The new church in the classical style had five domes and dimensions of 21 meters in length, 15 in width, and 38 in height. It was not heated. Arzamas writer and local historian Yeremeyev suggested that the project author was architect M. P. Korinthsky, who created the Resurrection Cathedral in Arzamas.

Simultaneously with the construction of the church, the monastery's water supply was being built. Water from the spring under the church was pumped up. This was done using a machine with a single-horse drive. A water tank with a capacity of 500 buckets was located in the northeast corner tower, which was named the Water Tower. From the tank, water was supplied through wooden pipes to the kvass brewery, bakery, hospital, and other buildings. The cast-iron parts of the water-lifting machine were manufactured at the Vyksa plant in 1823. The water supply was designed and built by master Yegor Mikhailov, a carpenter from Nizhny Novgorod province, who moved to Sarov Desert in 1841 and took monastic vows in 1845 under the name Mikhail. All construction work in the monastery in the 1840s was carried out under his supervision, including the reconstruction of churches and the construction of a merchant hotel.

The spring under the Church of John the Baptist was used not only for the water supply. On holidays, a procession was held to the basin where the spring was enclosed, and prayers with water consecration were served.

In 1893, the vaults over the well under the church were finished and painted, and the arches were closed with glazed grilles. The year before, in 1892, the slope of the hill near the church was reinforced with brickwork and buttresses.

During the Soviet years, the church building was used for administrative purposes, and the spring of the Originator was filled and sealed. The Church of John the Baptist has survived in a modified form: the domes were demolished, and the interior volume was divided into floors. During the restoration of the church, the spring of the Originator was found and restored, including the ancient larch crowns of the well structure. The restoration was completed at the end of July 2006. During the celebration of the 300th anniversary of the founding of the Sarov Desert, the Church of John the Baptist was re-consecrated by His Holiness Patriarch Alexy II of Moscow and All Russia.