The monastery was founded in 1613 by monk Euphemius, who moved from Veliky Ustyug and brought with him an icon of the Mother of God. This icon, later named Seven Lakes, became known in 1654 when, it is believed, it saved people from a plague. In memory of these events, an annual procession from the Seven Lakes Monastery to Kazan was established on June 25.

Due to the veneration of the icon, the monastery began to receive generous donations. With these funds, the stone Smolensky Cathedral, the main church of the monastery where the icon was kept, was built in 1668. Now only the ruins of the basement floor remain. Even earlier, in 1640, the first stone church, the Ascension Church, was erected.

In the 19th century, three more churches and a multi-tiered bell tower were added to these buildings. The sixth church, dedicated to the icon of the Mother of God "Joy of All Who Sorrow," was built over a holy spring a kilometer from the monastery.

The monastery was one of the wealthiest in the Kazan diocese. In the 18th century, it owned more than 500 peasant souls. After the 1764 reform, when monasteries lost lands with peasants, the Seven Lakes Monastery was classified as III class. By the early 20th century, there was a church-parish school, two wooden inns, and a guesthouse operating here.

From 1884, the monastery was under the administration of the Kazan archbishop.

The brotherhood of the monastery in the 18th and 19th centuries numbered several dozen, sometimes reaching 100. Three processions were held annually: on June 25 to Kazan with the Seven Lakes icon of the Mother of God, on June 27 returning with the icon from Kazan, and on July 16 to the spring near the Sorrowful Church of the monastery.

From 1883 until May 1908, Elder Gabriel Zyryanov lived in the monastery, who was glorified as a locally revered saint in 1996.

The last abbot of the monastery before its closure, Archimandrite Alexander, was also canonized as the Blessed Alexander of Seven Lakes Sanaksar.

In 1928, the monastery was closed and destroyed, almost all its buildings, including the main cathedral and bell tower, were demolished. The surviving structures were used for the needs of the local state farm.

In 1996, the territory of the monastery was returned to the Russian Orthodox Church. Now the brotherhood of the monastery is small.

Of all the churches of the monastery, only a small church of Saints Euphemius the Great and Tikhon of Zadonsk has survived and been restored. It houses the relics of Gabriel of Seven Lakes, as well as a revered copy of the Seven Lakes icon of the Mother of God. The original icon is now kept in the Peter and Paul Cathedral of Kazan.