Superconducting niobium serves as a key enabling material for superconducting radio frequency (SRF) technology as well as quantum computing devices. Niobium has a high propensity for the uptake of hydrogen. At room temperature, hydrogen commonly occupies tetragonal sites in the Nb lattice as the metal (M) - gas (H) phase. When the temperature is decreased, however, a solid solution of Nb-H begins to precipitate. In this study, we show the first identified topographical features associated with nanometer-size hydride phase (Nb1-xHx) precipitates on the surface of the metallic superconducting niobium using cryogenic-atomic force microscopy (AFM). Further, high energy grazing incidence X-ray diffraction reveals information regarding the structure and stoichiometry of these precipitates. Finally, through time-of-flight secondary ion mass spectroscopy (ToF-SIMS), we locate atomic hydrogen sources near the top surface. This systematic study further explains localized degradation of RF superconductivity by the proximity effect due to hydrogen clusters.