And the those who drowned you will, in the end, be drowned themselves. Hillel didn't literally see a skull floating on the water. The use of the metaphors of the skull and the water represent these points. The head of the human being is his foundation, like the root of the tree, from which everything received its nourishment and sustenance.
Water represents the process of washing something away.
This never happens to righteous people, for even when they die they leave behind a legacy, and their deeds continue to have an impact. Flowing water washes something away, and the original water is then itself washed away by other water which follows, and so on. We can therefore say that whatever effects the process of washing away is itself washed away. Therefore, the Mishna describes a skull on the surface of the water, rather than on the ground, for this pattern of washing something away and then being washed away itself is unique to water. One may try to rid oneself of an enemy or a nuisance.