A method [joint reflectance and gas estimator (JRGE)] is developed to estimate a set of atmospheric gas concentrations in an unknown surface reflectance context from hyperspectral images. It is applicable for clear atmospheres without any aerosol in a spectral range between approximately 800 and 2500 nm. Standard gas by gas methods yield a 6% rms error in H2O retrieval from Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data, reaching several tens percent for a set of widespread ground materials and resulting from an simplifying assumption of linear variations of the reflectance model within gas absorption bands and partial accounting of the gas induced signal. JRGE offers a theoretical framework consisting in a two steps algorithm that accounts for sensor characteristics, assumptions on gas concentrations and reflectance variations. It estimates variations in gas concentrations relatively to a standard atmosphere model. An adaptive cubic smoothing spline like estimation of the reflectance is first performed. Concentrations of several gaseous species are then simultaneously retrieved using a nonlinear procedure based on radiative transfer calculations. Applied to AVIRIS spectra simulated from reflectance databases and sensor characteristics, JRGE reduces the errors in H2O retrieval to 2.87%. For an AVIRIS image acquired over the Quinault prescribed fire, far field CO2 estimate (348 ppm, about 6% to 7% rms) is in agreement with in situ measurement (345-350 ppm) and aerosols yield an underestimation of total atmospheric CO2 content equal to 5.35% about 2 km downwind the fire. JRGE smoothes and interpolates the reflectance for gas estimation but also provides nonsmoothed reflectance spectra. JRGE is shown to preserve various mineral absorption features included in the AVIRIS image of Cuprite Mining District test site.