Nanostructured WO3 photoanodes have been synthesized by electrochemical anodization under controlled hydrodynamic conditions in acidic media in the presence of 0.05 M H2O2. Subsequently, samples have been subjected to a thermal treatment (annealing) at different temperatures (400 °C, 500 °C and 600 °C) and under different gaseous atmospheres (air, N2, Ar). The influence of these annealing conditions on the morphology, crystallinity, photoelectrochemical behavior and dopant chemistry of the different photoanodes has been investigated through Electronic Microscopy, Raman Spectroscopy, Photoelectrochemical Impedance Spectroscopy and Mott-Schottky analysis. In general, higher annealing temperatures resulted in samples with higher degrees of crystallinity, which in turn favored the transport of electron-hole pairs through the semiconducting photoanodes. Besides, an increase in annealing temperature implied higher densities of donor species within the samples structure, which can explain the observed enhancement in charge transfer. Annealing temperature was observed to have a more marked impact on the photoelectrocatalytic performance of WO3 nanostructures than the gaseous atmosphere.