Silicon oxynitride (SiOxNy) films were deposited by electron cyclotron resonance plasma enhanced chemical vapor deposition (ECR-PECVD) and covered the entire composition range from silicon dioxide to silicon nitride. The composition of the films was determined by Rutherford backscattering spectroscopy (RBS), nuclear reaction analysis (NRA), and elastic recoil detection (ERD). These techniques provide the absolute areal concentrations of all elements, including silicon, oxygen, nitrogen, and hydrogen. Additionally, Fourier transform infrared (FTIR) spectroscopy and ellipsometry measurements were performed for the optical characterization of the thin films. Effective medium theories (EMT) were used to model the optical and compositional properties of the SiOxNy films. The refractive index measured by ellipsometry was compared with theoretical calculations using Maxwell–Garnett and Bruggeman equations. The experimental results agree quite well with model data. It is also shown that the concentration of hydrogen in the films has a major influence on the quality of the agreement.