The structural changes in Ru-coated Y films during hydrogenation were studied in this work. In situ XRD data were used to show that the Y to YH2 transition requires significant hydrogen loading of the Y lattice. By comparing the XRD data with the in situ spectroscopic ellipsometry data, an effective medium model for the transition was obtained. This model describes the Y to YH2 transition well. The YH2 to YH3 transition is also described by an effective medium model, however, with reduced accuracy around the midpoint of the transition. By comparing the YH2 and YH3 crystal sizes, we show that these deviations may be due to a surface plasmon resonance. The improved understanding of the ellipsometry measurements is important for optical hydrogen sensing applications.