From Halopedia, the Halo wiki
Deuterium is an isotope of the chemical element hydrogen (chemical symbol H). The nucleus of protium (the most common form of Hydrogen) contains only the single proton, deuterium's nucleus contains one neutron in addition to the proton, and tritium's contains one proton and two neutrons. Deuterium nuclei produce a great deal of energy when fused together into helium nuclei. This is the fusion reaction that occurs in the sun and all other stars. Deuterium, along with tritium, is a primary fuel source for Covenant pinch fusion reactors and the UNSC's fusion reactors, including those used to power starships' fusion drives.
Deuterium has a natural abundance on planet surfaces, such as on Earth and Pegasi Delta. The Covenant build refineries to refine this material for use in their ships. It is also used in UNSC ships and stations to power the onboard reactors and, should the need arise, facilitate self-destruction by flooding the reserve tanks into the reaction chamber.