Superconducting niobium serves as a key enabling material for superconducting radio frequency (SRF) technology as well as quantum computing devices. At room temperature, hydrogen commonly occupies tetragonal sites in the Nb lattice as metal (M)-gas (H) phase. When the temperature is decreased, however, solid solution of Nb-H starts to be precipitated. In this study, we show the first identified topographical features associated with nanometer-size hydride phase (Nb1-xHx) precipitates on metallic superconducting niobium using cryogenic-atomic force microscopy (AFM). Further, high energy grazing incidence X-ray diffraction reveals information regarding the structure and stoichiometry that these precipitates exhibit. Finally, through time-of-flight secondary ion mass spectroscopy (ToF-SIMS), we are able to 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.