The goal of this work was to demonstrate the use of Tunable Diode Laser Absorption Spectroscopy (TDLAS) as a noninvasive method to continuously measure the water vapor concentration and the vapor flow velocity in the spool connecting a freeze‐dryer chamber and condenser. The instantaneous measurements were used to determine the water vapor mass flow rate (g/s). The mass flow determinations provided a continuous measurement of the total amount of water removed. Full load runs of pure water at different pressure and shelf temperature settings and a 5% (w/w) mannitol product run were performed in both laboratory and pilot scale freeze dryers. The ratio of “gravimetric/TDLAS” measurements of water removed was 1.02 ± 0.06. A theoretical heat transfer model was used to predict the mass flow rate and the model results were compared to both the gravimetric and TDLAS data. Good agreement was also observed in the “gravimetric/TDLAS” ratio for the 5% mannitol runs dried in both freeze dryers. The endpoints of primary and secondary drying for the product runs were clearly identified. Comparison of the velocity and mass flux profiles between the laboratory and pilot dryers indicated a higher restriction to mass flow for the lab scale freeze dryer. © 2007 Wiley‐Liss, Inc. and the American Pharmacists Association J Pharm Sci 96: 1776–1793, 2007