It belonged to the district of Zamoskvorechye, south of the river, and became an urban area much later than the left bank of the river, where the Kremlin is located. The square was frequently used for public executions, notably, the famous rebel Stepan Razin in 1671 and Yemelyan Pugachev, a leader of a peasant rebellion, who was executed there in 1775. It was also the last public execution in the square. The area was flooded on a regular basis until the 1780s, when the Vodootvodny Canal was dug to normalize the situation. In the 19th century, the area was built up by the addition houses and warehouses of local merchants, some of which are still intact.
In 1958, the monument to Ilya Repin was built in the center of the square. In 1962, the square was renamed Repin Square. In 1994, together with other streets and squares of the historical center of Moscow, it was renamed back to Bolotnaya Square. In 2001, the sculpture group of Children Are the Victims of Adult Vices by Mihail Chemiakin was unveiled on the square.