Ganymede’s atmosphere is produced by charged particle sputtering and sublimation of its icy surface. Previous far-ultraviolet observations of the O i 1,356 Å and O i 1,304 Å oxygen emissions were used to infer sputtered molecular oxygen (O2) as an atmospheric constituent, but an expected sublimated water (H2O) component remained undetected. Here we present an analysis of high-sensitivity spectra and spectral images acquired by the Hubble Space Telescope revealing H2O in Ganymede’s atmosphere. The relative intensity of the oxygen emissions requires contributions from the dissociative excitation of water vapour, indicating that H2O is more abundant than O2 around the subsolar point. Away from the subsolar region, the emissions are consistent with a pure O2 atmosphere. Eclipse observations constrain atomic oxygen to be at least two orders of magnitude less abundant than these other species. The higher H2O/O2 ratio above the warmer trailing hemisphere compared with the colder leading hemisphere, the spatial concentration in the subsolar region and the estimated abundance of ~1015 molecules of H2O per cm2 are consistent with sublimation of the icy surface as source.