Silicon oxide, silicon nitride and silicon oxynitride layers were grown by a PECVD technique. The resulting refractive indices of the layers varied between 1.47 and 1.93. The compositional properties of the layers were analyzed by FTIR and ATR infrared spectroscopy techniques. Comparative investigation of bonding structures for the three different layers was performed. Special attention was given to analyze N-H bond stretching absorption at 3300-3400 cm(-1). Quantitative results for hydrogen related bonding concentrations are presented based on IR analysis. An annealing study was performed in order to reduce or eliminate this bonding types. For the annealed samples the N-H bond concentration was strongly reduced as verified by FTIR transmittance and ATR spectroscopic methods. A correlation between the N-H concentration and absorption loss was verified for silicon oxynitride slab waveguides. Moreover, a single mode waveguide with silicon oxynitride core layer was fabricated. Its absorption and insertion loss values were determined by butt-coupling method, resulting in low loss waveguides.