Suiten-gu Shrine was originally a temple sacred to Buddhism's god Suiten, but Suiten was replaced with Ame no Minakanushi no Kami at the time of the separation of Buddhism and Shintoism, based on the notion that the divinity of Varuna (a god from whom Suiten derived) was the primordial god and so was that of Ame no Minakanushi no Kami in the Kojiki and Nihonshoki mythology.
水天宮は、元は仏教の神・水天を祀るものであるが、神仏分離の際、水天の元となったヴァルナ(神)の神格が始源神であることから、記紀神話における始源神・天之御中主神に置き換えられたものである。