We have measured the concentration of deuterium as a function of depth in a deuterium‐exchanged LiNbO3sample using nuclear analysis. From the shape of the concentration profile we calculate the concentration dependent effective diffusion coefficient for deuterium‐lithium counterdiffusion. Comparison of the concentration and refractive index profiles for this waveguide confirms that the index increase in exchanged material is a nonlinear function of concentration. We discuss implications of these results for optical waveguide fabrication.