When Indra, King of the Heavens saw that Krishna had encouraged the Vrajavasis to no longer worship him, and to worship Govardhan Hill instead, he became angry and decided to destroy them all with torrential rains and thunderbolts. When after seven days he was still not successful in killing them all as Krishna had kept them safe under Govardhan Hill, Lord Brahma advised him to stop with his anger and ask forgiveness for his offenses. Following Lord Brahma's advice, Lord Indra asked Mother Surabhi, the celestial cow, to join him and he used her milk to perform the abhisheka bathing ceremony of Krishna's feet and offered prayers. In this ceremony, he also used Ganges water, tulasi manjaries, and lotus flowers with Surabhi's milk, and these ingredients use to always fill this kunda. 

Krishna's great-grandson Sri Vajranabha established this kunda in memory of these pastimes, and in the Mathura-khanda it is stated: "Simply by bathing in Govinda Kunda, one is awarded liberation."