Correct estimation of soil and vegetation thermal emissivities is of huge importance in remote sensing studies. It has been shown that the emissivity of leaves retrieved from field observations show subtle spectral features that are related to leaf water content. However, such field measurements provide additional challenges before leaf water content can be successfully obtained, specifically atmospheric correction. The aim of this research was to investigate how information within hyperspectral thermal observations can be used to auto-correct the atmospheric influence. Hyperspectral thermal measurements were taken over a large variety of soil and vegetation types (including vineyard and barley) during ESA’s REFLEX campaign in 2012 using a MIDAC FTIR radiometer. Using MODTRAN simulations, a simple quadratic model was constructed that emulates the atmosphere radiative transfer between the target and the sensor. Afterwards, this model was used to estimate the concentrations of H20 (g) and CO2 (g) while simultaneously correcting for these gas absorptions. Finally, a temperature-emissivity separation was applied to estimate the emissivities of the different land surface components.The uncertainty of the approach was evaluated by comparing the retrieved gas concentrations against parallel measurements of a LICOR 7500. It was found that most measurements of gas concentrations were successfully retrieved, with uncertainties lower than 25%. However, absolute correction of the absorption features proved more difficult and resulted in overestimations of the correction-terms. This was mainly due to overlapping of spectral features with the observations in the simulations that proved troublesome.