waveguide resonator chips using the same microfabrication procedures and solvent cleans. The samples were then subject to different acid cleaning treatments using different combinations of piranha, hydrofluoric acid, and buffered oxide etch solutions. The different samples expressed changes in dc resistivity in the normal and superconducting states such that the low temperature resistivities changed by more than 100\%, and the residual resistivity ratio dropped by a factor of 2. The internal quality factor of coplanar waveguide resonators measured near 5~GHz also showed significant variation at single photon powers ranging from 1.4×106 to less than 60×103. These changes correlate with the formation of surface crystallites that appear to be hydrocarbons. All observations are consistent with hydrogen diffusing into the niobium film at levels below the saturation threshold that is needed to observe niobium hydrides.