The water molecule has two hydrogen atoms held at an angle of 104° 27' and at distances of nearly 0.1 nm from the oxygen atom. The hydrogen atoms are held at about 0.1 nm from each other. The molecule is covalently bonded, electrons being shared between the hydrogens and the oxygen, giving overall electrical neutrality, but the oxygen nucleus has greater affinity for electrons than that of the hydrogen. There is thus, on average, a slight displacement of negative charge towards the oxygen, which leaves a slight positive charge on the hydrogen atoms. Consequently there is an attraction between the slightly positive hydrogen on one molecule, and the slightly negative oxygen on the other, which links them together with a 'hydrogen bond'. The angles at which oxygen and hydrogen are held in the water molecule, coupled with this hydrogen bonding, result in a crystal structure for ice that is based on tetrahedra.

Oxygen is at the centre of each tetrahedron, surrounded by four hydrogen atoms, two covalently and two hydrogen-bonded. Such a crystal is quite open, compared with those of other substances, which often have twelve neighbours (as opposed to four in ice) packed around each molecule, Ice consequently has a low density. It floats on liquid water and, by forming an insulating layer at the surface of water bodies, often prevents them from freezing solid and thus killing fish and other organisms.

The hydrogen bonding in ice is quite strong, because the displacement of negative charge towards the oxygen atom is powerful. The temperature at which melting of ice takes place - a measure of the energy needed to begin breaking down the hydrogen-bonded structure - is thus relatively high, compared with H₂S and H₂Se, where the charge displacement in the molecules is small.