First results from the Neutral Gas and Ion Mass Spectrometer instrument on the Mars Atmosphere and Volatile EvolutioN (MAVEN) spacecraft reveal density profiles of protonated species that are mostly in good qualitative agreement with recent models of the Martian thermosphere/ionosphere. We present here the first photochemical model in which the density profiles of water and water ions in the ionosphere/thermosphere are predicted. We find that the computed peak densities of OH+, H2O+, and H3O+ are in fairly good agreement with the measured values. The computed column density of water is predicted to be about 1010 cm−2, and the mixing ratio at 80 km is 0.4 ppb. The actual water densities must be small enough so that HCO+ is not destroyed by proton transfer to water during the daytime and large enough so that H3O+ dominates the ionosphere at low altitudes just beyond the terminator. The calculations also show that the mass‐2 ion is almost certainly H 2+. Key Points We preset the first model of water in the Martian thermosphere The predicted density profiles of H2O, H2O+, and H3O+ are presented We predict that H 2+ is the mass‐2 ion rather than D+