Changes in the hydrogen content and bonding in amorphous hydrogenated silicon (a-Si:H) films during stepwise thermal annealing are measured using in situ real time infrared spectroscopy. The experimental spectra are fit using previously identified SiH stretching modes for hydrogen bonded at isolated network sites, hydrogen in platelet-like configurations and hydrogen at surfaces. Based on this mode separation, the release of hydrogen from surfaces and platelet configurations is found to occur at ∼320–370°C. By 470°C, these groups are completely released from the sample, whereas isolated SiH network sites are still present. This thermal annealing of the sample also irreversibly changes the microstructure and thereby the distribution of available hydrogen bonding sites in the amorphous network. Re-hydrogenation experiments show that isolated bonding sites are created and platelet and surface bonding sites are removed from the hydrogen density of states. This structural transformation during annealing is interpreted as the release of hydrogen from platelet like configurations and the reformation of Si–Si bonds in a-Si:H.