The isotope effect is an important topic that is relevant for future D-T fusion reactors, where the use of deuterium, rather than hydrogen, may lean to improved plasma confinement. An evaluation of the ratio of hydrogen/deuterium is needed for isotope effect studies in current isotopic experiments. Here, the spectral range around Hα and Dα lines, obtained with an intensified multi-channel detector mounted to a 1-m focal length spectrometer, is analyzed using a fit function that includes several Gaussian components. The isotopic ratio evolution for a single operational day of the TJ-II stellarator is presented. The role of injected hydrogen by Neutral Beam Injection heating is also studied.