Sodium hexatitanate (Na2Ti6O13) nanoparticles have been synthesized by the hydrothermal method with microwave and conventional heating, after which their photocatalytic properties toward an azo dye pollutant degradation have been investigated. Insights into the dynamics and reactivity of the species involved in the photocatalytic mechanism of the (Na2Ti6O13) samples were precisely investigated, for the first time, by X-band electron paramagnetic resonance (EPR) spectroscopy under different experimental conditions. X-ray diffraction structural analysis revealed that all samples crystallized in a monoclinic C2/m structure, with different short-range structural order according to the employed heating, as indicated by Raman. Field-emission scanning electron microscopy and transmission electron microscopy results revealed the formation of rod- and fiber-like nanoparticles with different diameters and lengths. EPR measurements indicated the presence of different Ti3+ point defects and F centers in the samples. X-ray photoelectron spectroscopy analysis proved the presence of oxygen-related defects, but no Ti3+ was detected on the surface. Spin trapping experiments monitored the generation of hydroxyl (OH·) radicals over UV-irradiation time. Various parameters contribute to the photocatalytic activity of the samples; however, the type of defect and particle morphology appeared as key factors for enhanced efficiency. Our study provides significant information about paramagnetic defects in Na2Ti6O13 materials and their role in photocatalysis to design other Ti-based photocatalysts.