No. Neither is a metaphor. From http://www.thefreedictionary.com/face :why are you willing to accept that "face of the waters" is a metaphor but "day" is not?
Face - 8. The most significant or prominent surface of an object, especially:
a. The surface presented to view; the front.
b. A fašade.
c. Outer surface: the face of the earth.
"She is the apple of my eye" is a metaphor. Eyes don't have an apple. The water has a face, just like a building and a clock.