The performance of free-space optical applications can be improved using beams of different wavelengths for the auxiliary actions of pointing/tracking or turbulence correction. Chromatic dispersion owing to the atmosphere is an issue for multiwavelength systems, and the dispersion of electromagnetic signals is typically predicted based on refractive conditions from standard atmospheric models. However, for long near-horizontal paths near the Earth’s surface, substantial refractive index gradients that are associated with features such as inverse temperature layers and ducts can be encountered. These features can significantly alter the ray trajectory, the chromatic divergence, and the angle of arrival of directional beams relative to standard atmosphere predictions. A ray tracing approach was implemented to examine the chromatic divergence and angle of arrival of the rays through various practical and extreme atmospheric conditions involving a temperature inversion layer. Over a distance of 150 km along the ground, a brief encounter with the layer can cause pairs of rays with wavelengths 532 and 1550 nm to diverge up to 4.5 times greater than their standard atmosphere predictions. For a single wavelength, a linear increase of angle of arrival with initial launch angle was found for the standard atmosphere, but this trend was significantly altered in the presence of an inversion layer. Extreme refractive conditions with a large inversion layer were simulated to produce optical ducting over long distances. Chromatic separation of rays as large as 280 m was observed when only one of the two wavelengths remained in the duct.