The identification of defects and their controlled generation in titanate nanostructures is a key to their successful application in photoelectronic devices. We comprehensively explored the effect of vacuum annealing on morphology and composition of Na2Ti3O7 nanowires and protonated H2Ti3O7 nanoscrolls using a combination of scanning electron microscopy, Auger and Fourier-transform infrared (FT-IR) spectroscopy, as well as ab initio density functional theory (DFT) calculations. The observation that H2Ti3O7 nanoscrolls are more susceptible to electronic reduction and annealing-induced n-type doping than Na2Ti3O7 nanowires is attributed to the position of the conduction band minimum. It is close to the vacuum level and, thus, favors the Fermi level-induced compensation of donor states by cation vacancies. In agreement with theoretical predictions that suggest similar formation energies for oxygen and sodium vacancies, we experimentally observed the annealing induced depletion of sodium from the surface of the nanowires.