Wat Phou was initially associated with the city of Shrestapura, which lay on the bank of the Mekong directly east of mount Lingaparvata (now called Phu Kao). By the latter part of the 5th century the city was already the capital of a kingdom which texts and inscriptions connect with both Chenla and Champa, and the first structure on the mountain was constructed around this time. The mountain gained spiritual importance from the linga-shaped protuberance on its summit; the mountain itself was therefore considered the home of Shiva, and the river as representing the ocean or the Ganges River. The temple was naturally dedicated to Shiva, while the water from the spring which emerges directly behind the temple was considered sacred.
Wat Phou was a part of the Khmer empire, centred on Angkor to the southwest, at least as early as the reign of Yashovarman I in the early 10th century. Shrestapura was superseded by a new city in the Angkorian period, located directly south of the temple. In the later period, the original buildings were replaced, re-using some of the stone blocks; the temple now seen was built primarily during the Koh Ker and Baphuon periods of the 11th century. Minor changes were made during the following two centuries, before the temple, like most in the empire, was converted to Theravada Buddhist use. This continued after the area came under control of the Lao, and a festival is held on the site each February. Little restoration work has been done, other than the restoration of boundary posts along the path. Wat Phou was designated a World Heritage Site in 2001.