Iron oxide nanostructures are an attractive option for being used as photocatalyst in photoelectrochemical applications such as water splitting for hydrogen production. Nanostructures can be obtained by different techniques, and electrochemical anodization is one of the simplest methods which allows high control of the obtained morphology by controlling its different operational parameters. In the present study, the influence of the electrolyte temperature during electrochemical anodization under stagnant and hydrodynamic conditions was evaluated. Temperature considerably affected the morphology of the obtained nanostructures and their photoelectrochemical behavior. Several techniques were used in order to characterize the obtained nanostructures, such as Field Emission Scanning Electron Microscopy (before and after the annealing treatment in order to evaluate the changes in morphology), Raman spectroscopy, photocurrent vs. potential measurements and Mott-Schottky analysis. Results revealed that the nanostructures synthesized at an electrolyte temperature of 25 °C and 1000 rpm are the most suitable for being used as photocatalysts for water splitting.