"and the Spirit of G-d hovering over the water's surface."
This expression refers to The Throne of Divine Glory, which was poised in space, hovering over the water's surface, by means of the ruach (breath) of G-d's mouth and through His word - like a dove hovering over the nest. (Rashi)
A spirit of grace and loving kindness emanating from G-d and hovering over the waters, as much as to say that the Shechinah (the Divine Presence) in Divine tranquility was engaged in bringing order into the chaos. (Targum Yerushalmi; Rashi)
And the Ruach of G-d hovered over the face of the waters - Tohu (unformed) is colorless, nondescript place; bohu (void) is one that has shape and form. Choshech (darkness) is black fire of deepest hue, deep red fire, bright green fire, and white fire, which comprises all the other hues. Choshech is a fire which ceased to be pure black when it overwhelmed tohu. Ruach (wind) is a sound which hovers over bohu and seizes and leads it wherever it is required. That is the esoteric meaning of he verses, "The voice of Hashem is upon the waters" (Tehillim 29:3); and similarly, "And the ruach of G-d hovered over the face of the waters." (Zohar 1:16)
Source: Chok L'Yisrael; Torah Shlemah
