Chemical and structural defects have a profound impact on the performance of niobium superconducting radio frequency cavities for particle accelerators. The properties of the first 40-100 nm of the cavity sub-surface determine the performance of the cavity because of the expulsion of the magnetic field in the superconducting state due to the Meissner effect. Chemical impurities present in this region that are introduced during standard fabrication techniques can severely hinder, or improve, cavity performance. Dissolved hydrogen in the cavity can precipitate out as niobium hydride phases on the cavity surface and cause local areas of reduced superconductivity or even quench if the hydrides are large enough. The interaction of hydrogen with other impurities affects the growth of hydride phases during cooldown. Many decades of R&D have now gone into developing surface treatments for the cavities to optimize performance. This thesis focused on two projects that were each directly motivated by surface treatments for Nb SRF cavities that revolutionized cavity performance. Simply baking the cavities in a UHV furnace, or even in air, at very mild temperatures of 400-440 K eliminates the onset of the so called high Q drop-off on standard electropolished cavities. Given the mild temperature of this procedure, oxygen dissolution is likely to play a role. Nitrogen doping the cavities at the end of the UHV hydrogen degas has even more profound effects on cavity performance. Q is increased at all accelerating gradients, there is a reversal of the field dependence of Q in the medium field regime, and the high Q drop off is eliminated. The role of nitrogen in possibly suppressing the formation of nanoscale hydride features is the subject of intense interest and study in the SRF community. The dissolution of the native niobium pentoxide layer was studied with Auger electron spectroscopy. An activation energy for oxygen dissolution from the surface into the bulk was calculated. The (3x1)-O ladder structures were characterized with scanning tunneling microscopy before and after dissolution, and surface reconstructions of the ladders were observed after repeated oxygen dissolution. Nb(100) crystals were doped with hydrogen, nitrogen and hydrogen, and nitrogen only. Hydride growth and suppression were studied with scanning tunneling microscopy and scanning tunneling spectroscopy by cooling and holding the crystals at 100 K in the microscope stage through the use of a continuous flow liquid helium cryostat. Surface structural evolution and changes to the surface bandgap measured via STS were tracked over the course of many days while the crystal was kept cold. The surface bandgap was shown to significantly narrow relative to the blank ladders on the hydrogen doped surface. Additionally, the surface bandgap of the nitrogen as well as nitrogen and hydrogen infused sample widened relative to undoped Nb(100) at 100 K. These results provide the first structural and electronic characterization of initial Nb hydride growth and suppression behavior at the nano-scale.