We present a Bayesian estimation analysis for a particular trace gas detection technique with species separation provided by differential diffusion. The proposed method collects a sample containing multiple gas species into a common volume, and then allows it to diffuse across a linear array of optical absorption detectors, using, for example, high-finesse Fabry-Perot cavities. The estimation procedure assumes that all gas parameters (e.g. diffusion constants, optical cross sections) are known except for the number population of each species, which are determined from the time-of-flight absorption profiles in each detector.