<p>We have developed a spectral fitting method to retrieve upper atmospheric parameters at multiple altitudes simultaneously during times of aurora, allowing us to measure neutral temperatures and column densities of water vapour. We use the method to separate airglow OH emissions from auroral O<sup>+</sup> and N<sub>2</sub> in observations between 725–740 nm using the High Throughput Imaging Echelle Spectrograph (HiTIES), located on Svalbard. In this paper, we describe our new method and show the results of Monte-Carlo simulations using synthetic spectra which demonstrate the validity of the spectral fitting method as well as provide an indication of uncertainties on the retrieval of each atmospheric parameter.</p>