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Superconducting niobium (Nb) thin films have recently attracted significant attention due to their utility for quantum information technologies. In the processing of Nb thin films, fluoride‐based chemical etchants are commonly used to remove surface oxides that are known to affect superconducting quantum devices adversely. However, these same etchants can also introduce hydrogen to form Nb hydrides, potentially negatively impacting microwave loss performance. Here, comprehensive materials characterization of Nb hydrides formed in Nb thin films as a function of fluoride chemical treatments is presented. In particular, secondary‐ion mass spectrometry, X‐ray scattering, and transmission electron microscopy reveal the spatial distribution and phase transformation of Nb hydrides. The rate of hydride formation is determined by the fluoride solution acidity and the etch rate of Nb2O5, which acts as a diffusion barrier for hydrogen into Nb. The resulting Nb hydrides are detrimental to Nb superconducting properties and lead to increased power‐independent microwave loss in coplanar waveguide resonators. However, Nb hydrides do not correlate with two‐level system loss or device aging mechanisms. Overall, this work provides insight into the formation of Nb hydrides and their role in microwave loss, thus guiding ongoing efforts to maximize coherence time in superconducting quantum devices. [ABSTRACT FROM AUTHOR]