Performance of terrestrial and vertical Free-Space Optical (FSO) communication systems are strongly influenced by the atmospheric boundary layer (ABL) dynamics. In addition to the diurnal variations in the refractive index structure parameter (Cn2 ) caused by the wind speed and the temperature difference between the surface and the near-surface air mass, any other unprecedented temperature variations can lead to Cn2 variations. Even though the prevailing ‘simple’ Cn2 models capture the overall trend in vertical Cn2 variations, they fail to capture the effects of temperature inversions, especially in tropical regions. Influence of absorbing aerosols like Black Carbon (BC), which can improve the atmospheric stability by forming strong temperature inversion layers, are not considered in these models. BC can reduce the optical beam intensity by scattering and absorption and can also cause variations in refractive index by modifying the local temperature. The uncertainties in the implications of BC will be large, owing to their large spatio-temporal and vertical variations. Using high-resolution balloon measurements and multi-satellite observations coupled with a radiative transfer model, we substantiate the strong influence of absorbing aerosols on the vertical distribution of Cn2 . We report how vertical profiling of absorbing aerosols can be used to estimate altitudes with low refractive index fluctuations. The manifestations of high-altitude aerosol-induced atmospheric warming in FSO systems are also pointed out. We conclude by discussing how mass concentration of BC, a good tracer for ABL dynamics, is correlated with the near-surface refractive index fluctuations.