In infrared species tomography, the unknown concentration distribution of a species is inferred from the attenuation of multiple collimated light beams shone through the measurement field. The resulting set of linear equations is rank-deficient, so prior assumptions about the smoothness and nonnegativity of the distribution must be imposed to recover a solution. This paper describes how the Kalman filter can be used to incorporate additional information about the time evolution of the distribution into the reconstruction. Results show that, although performing a series of static reconstructions is more accurate at low levels of measurement noise, the Kalman filter becomes advantageous when the measurements are corrupted with high levels of noise. The Kalman filter also enables signal multiplexing, which can help achieve the high sampling rates needed to resolve turbulent flow phenomena.