The water and trace element contents of natural igneous zircons were determined to constrain the mechanism of hydrogen incorporation. The low radiation-damage zircons were derived from Fe–Ti oxide gabbros from the Vema Fracture Zone (11°N, Mid-Atlantic Ridge). They contain up to 1212 ppmw H2O, 1.9 wt.% Y2O3 and 0.6 wt.% P2O5 and are generally strongly zoned. REE + Y are partially charge-balanced by P (Y, REE3+ + P5+ = Zr4+ + Si4+), but a large REE excess is present. On an atomic basis, this excess is closely approximated by the amount of H present in the zircons. We therefore conclude that H is incorporated by a charge-balance mechanism (H+ + REE3+ = Zr4+). This interpretation is consistent with FTIR data of the Vema zircons, which shows a strongly polarised main absorption band at ca. 3100 cm−1, similar to experimentally grown Lu-doped hydrous zircon. The size of this 3100 cm−1 band scales with H and REE contents. Apart from a small overlapping band at 3200 cm−1, no other absorption bands are visible, indicating that a hydrogrossular-type exchange mechanism does not appear to be operating in these zircons. Because of charge-balanced uptake of H, P and REE in zircon, the partitioning of these elements into zircon is dependent on each of their concentrations. For instance, DREEzrc/melt increases with increasing H and P contents of the melt, whereas DHzrc/melt increases with increasing REE content but decreases with increasing P content. In addition, H–P–REE systematics of sector zoning indicate kinetic effects may play an important role. Hence, using H in zircon to determine the water content of melts is problematic, and REE partitioning studies need to take into account P and H2O contents of the melt.