AbstractThis study focuses on the effects of polar mesospheric cloud (PMC) formation on the chemical environment of the mesosphere and lower thermosphere. Of specific interest is how the dehydration due to mesospheric ice particle formation leads to significant seasonal decreases in the atomic hydrogen near the mesopause at middle to high latitudes. Using a three‐dimensional whole atmosphere coupled chemistry/dynamics model, we simulate the effects of this dehydration, and via comparisons with three data sets taken from two NASA satellites, we quantify the perturbations to atomic hydrogen and water vapor. We also identify a local ozone maximum that results from the PMC‐induced decrease in atomic hydrogen. Further, the large interannual variability in the onset of the Southern Hemisphere PMC season correlates well with the interannual variability of early summer atomic hydrogen at 95 km. Since the PMC onset is known to be controlled by interannual variations in the Southern Hemisphere stratospheric polar vortex, this correlation indicates a coupling between the stratosphere and the chemistry of the mesosphere and lower thermosphere. Finally, our model results suggest that the seasonal biteout in atomic hydrogen propagates up into the thermosphere and to lower latitudes. This raises the intriguing possibility that PMC formation might play a role in modulating the escape of hydrogen from the atmosphere.