The fragments of comet Shoemaker--Levy-9 will enter the atmosphere of Jupiter during July 20--26, 1994. Significant amounts of water vapor will be injected into the upper atmosphere of Jupiter either from the comet itself or from the lower atmosphere of Jupiter. The photochemistry of both the neutral gas and the ionosphere will be greatly altered by the influx of this water vapor or the atomic oxygen generated by the dissociation of the water. Enhanced abundances of H2O (or other species such as NH3) in the atmosphere above the homopause should persist for at least a year and should be globally distributed. The odd oxygen (i.e., O or H2O or OH) associated with the cometary water influx alters the ion chemistry by removing H+ ions, which also has the effect of reducing the ionospheric electron density because H+ is ordinarily the main ion species in the Jovian ionosphere. The density of H+3, both in the auroral and non-auroral ionosphere, will also be reduced due to presence of water. This ion species has been detected spectroscopically at Jupiter, and a drop in its abundance should be detectable. The major ion species will become H3O+ which could reach a peak density as high as 104 cm-3 in the non-auroral ionosphere and 105 cm-3 in the auroral ionosphere. It should be possible to detect this ion species spectroscopically from Earth-based observatories. ¿ American Geophysical Union 1994