The atmosphere of Jupiter is mainly hydrogen and methane, with a large number of hydrocarbons calculated to be produced by photodissociation and subsequent reactions. It is assumed that oxygen is added by meteoroids. Recent studies have found that photochemistry does not explain the measured ratios of water to carbon monoxide, if it is assumed that water is the major constituent of meteoroids and vapourises. A possible explanation is that processes that occur during or soon after the meteoroid's passage change the proportions of the oxygen-bearing constituents. In this paper, the processes considered are dissociation, ionization of the original molecules and ionization of dissociated products. The difference between applying these processes in the bulk atmosphere and in the meteor trail itself is investigated, as is the possibility of methane being dissociated in a shock wave produced by the meteoroid. In all cases, there was no significant change to the predicted density of water at the height of a measurement. However, the density of hydroxyl relative to water differed depending on the assumed process, thus presenting the possibility that measurements of electron-driven emissions from hydroxyl could be used for remote sensing of the actual processes occurring.