Nanostructured niobium oxides and hydroxides are potential candidates for photochemical applications due to their excellent optical and electronic properties. In the present work the thermal stability of Nb3O7(OH) superstructures prepared by a simple hydrothermal approach is investigated at the atomic scale. Transmission electron microscopy and electron energy-loss spectroscopy provide insights into the phase transformation occurring at elevated temperatures and probe the effect of the atmospheric conditions. In the presence of oxygen, H2O is released from the crystal at temperatures above 500 °C, and the crystallographic structure changes to H-Nb2O5. In addition to the high thermal stability of Nb3O7(OH), the morphology was found to be stable, and first changes in the form of a merging of nanowires are not observed until 850 °C. Under reducing conditions in a transmission electron microscope and during electron beam bombardment, an oxygen-deficient phase is formed at temperatures above 750 °C. This transformation starts with the formation of defects in the crystal lattice at 450 °C and goes along with the formation of pores in the nanowires which accommodate the volume differences of the two crystal phases.