Yes, those black waters would be the deeper layers of the unconscious.
The animus impersonates the unconscious, as the anima impersonates it in a man’s case. Those ﬁgures are as if on the surface of the sea.
One could say the anima was the woman who emerges from the water, like Aphrodite arising from the foam of the sea in a shell.
And the animus is also in a way a spirit that hovers over the black waters and often represented as such; I have two pictures in my collection where the animus is depicted as a huge black bird hovering over the primordial waters.
As an impersonated of the unconscious, the natural function of the amimus here is to establish a communication between the conscious mind and the collective unconscious.
I admit it is somewhat diﬃcult to have a clear idea of these matters, but I think if you ﬁnd it in any way hard to understand it is on account of your conception of the collective unconscious.
You perhaps understand the collective unconscious intoo abstrace a sense, whereas it is extremely concrete. Carl Jung, Visions Seminar, Pages 124-125.