We studied the precipitable water vapour (PWV) content near Cerro Armazones and discuss the potential use of our technique of modelling the telluric absorption lines for the investigation of other molecular layers. The site is designated for the European Extremely Large Telescope (E-ELT) and the nearby planned site for the Cherenkov Telescope Array (CTA). Spectroscopic data from the Bochum Echelle Spectroscopic Observer (BESO) instrument were investigated by using line-by-line radiative transfer model (LBLRTM) radiative transfer models for the Earths atmosphere with the telluric absorption correction tool molecfit. All observations from the archive in the period from December 2008 to the end of 2014 were investigated. The dataset completely covers the El Nino event registered in the period 2009-2010. Models of the 3D Global Data Assimilation System (GDAS) were used for further comparison. Moreover, for those days with coincidence of data from a similar study with VLT/X-shooter and microwave radiometer LHATPRO data at Cerro Paranal, a direct comparison is presented. This analysis shows that the site has systematically lower PWV values, even after accounting for the decrease in PWV expected from the higher altitude of the site with respect to Cerro Paranal, using the average atmosphere found with radiosondes. We found that GDAS data are not a suitable method for predicting of local atmospheric conditions - they usually systematically overestimate the PWV values. Due to the large sample, we were furthermore able to characterize the site with respect to symmetry across the sky and variation with the years and within the seasons. This kind of technique of studying the atmospheric conditions is shown to be a promising step into a possible monitoring equipment for CTA.