Nb is an elemental superconductor with a critical temperature of 9.3 K and is widely used to fabricate superconducting radiofrequency (SRF) cavities for particle accelerators. However, microstructural defects in Nb, such as grain boundaries and dislocations, can act as pinning centers for magnetic flux that can degrade SRF cavity performance. Hydrogen contamination is also detrimental to SRF cavity performance due to the formation of normal conducting hydrides during cool down. In this study, disc shaped Nb bi-crystals extracted from a high-purity large-grain Nb slice were investigated to study the effects of grain boundaries, hydrogen, and dislocations on superconducting properties. Grain orientation and grain boundary misorientation were measured using Laue X-ray diffraction and electron backscattered diffraction (EBSD) analyses. Cryogenic magneto-optical imaging was used to directly observe magnetic flux penetration below T_c =9.3 K. Damage caused by low temperature precipitation of hydrides and their dissolution upon reheating after cryogenic cycles was examined using electron channeling contrast imaging (ECCI), and EBSD. The relationships between hydride formation, dislocation content, grain boundaries, cryo-cooling, heat treatment, and flux penetration indicate that both grain boundary character and hydrogen content affect magnetic flux penetration. Such flux penetration could be facilitated by dislocation structures and low angle grain boundaries resulting from hydride precipitation and heat treatment.