This research paper reports the results of application of near infrared spectroscopy and Aquaphotomics to the study of the structure of water in hydrogel materials of soft contact lenses. The purpose of this research was to study and describe changes in water structure within hydrogel materials with low, medium and high water content. Near infrared spectroscopy provides a rapid, non-destructive and reagent-free method of characterisation, while the Aquaphotomics approach to the analysis of the spectra of hydrated contact lenses provides identification of different water molecular species within the complex water structure of hydrogels. Our results show the possibilities of applying Aquaphotomics for better description of the states of water in hydrogels, with more information about water than the currently prevailing “three states” model.