This thesis uses H3+ spectroscopic observations of the Jovian ionosphere to characterise the physical conditions and dynamical processes within the aurorae. Five nights of observations were made using the CSHELL spectrometer on the NASA Infrared Telescope Facility, Mauna Kea, Hawaii. The spectrometer was set to a wavelength of 3.953 microns, sensitive to the molecular ion, a key component of the Jovian ionosphere. This provided an unprecedented level of detail on the processes within the Jovian aurora. The first astronomical detection of the H3+ (2v2(0) → V2) R(3,4+) hotband allowed the detailed calculation of the variations in vibrational temperatures across the auroral region, and from this the further calculation of column density and total emission. The data was obtained under conditions where the Jovian ionosphere was hotter than previously reported, by about 100°K to 200°K. The correspondence between emission intensity and column density proves that H3+ intensity is a strong indicator of the location of energy deposition. The further correspondence between total emission and H3+ intensity shows that H3+ is a stabilising agent within the Jovian aurorae. Thus, energy deposition is balanced by H3+ cooling, which explains the lack of correlation observed between temperature and H3+ emission. The CSHELL spectrometer produced spectra sensitive to Doppler shifts of as little as 300 m/s. A new observational technique was derived using a combination of spectroscopy and imaging, to take account of instrumental effects caused by spatial variations in the H3+ emission. Thus, a method of obtaining ion wind speeds from the Doppler shifting of H3+ emission lines is produced. It shows the existence of a regular electrojet around the main auroral oval, with speeds in the line-of-sight of around a few hundred m/s to 1 km/s, as well as a complex pattern of winds within the polar cap region.