Absorption is caused by molecules suspended in the terrestrial atmosphere interacting with an incident photon and absorbing some or all of its energy. Absorption is strongly correlated to both the type of molecule present and the concentration of the molecule. Water, carbon dioxide, oxygen, and ozone molecules all absorb strongly in the infrared region. This leads to windows in the infrared band where transmission is very high; there will also be windows where transmission is impossible. For example, carbon dioxide absorbs infrared light between 4.2 and 4.6 micrometers. If an FSO device tried to transmit in that waveband, the signal would be absorbed before it could be received. If an FSO tried to receive in that waveband, no signal would ever reach its detector.
Some atmospheric attenuation due to absorption can be truncated or ignored by selecting a wavelength with very low attenuation per kilometer, particularly in clear weather conditions. For adverse conditions, selecting the right wavelength that has the lowest attenuation per kilometer for that weather condition is crucial to establishing a transmittable signal. 
Turbulence is caused by wind and convection creating sections of air that have different temperatures inside them. Turbulence can lead to degradation in the quality of a transmitted optical beam. Turbulence also causes fluctuations in the density of air, leading to a change in the air refractive index. This causes beam refraction and beam spreading. The scale size of a turbulence cell can create different types of effects:
- If a turbulence cell has a larger diameter than an optical beam, then beam wandering is the dominant effect. Beam wandering is the displacement of an optical beam spot over a slow time scale, with slow meaning the distinct capture of beam displacement over a few seconds or several minutes.
- If a turbulence cell has a smaller diameter than an optical beam, then scintillation is the dominant effect.
Geometric losses (also called optical beam attenuation) are induced due to divergence of the beam spot during its propagation from transmitter to receiver. As a beam diverges, its power decreases. For laser sources, loss by divergence is negligible over short distances due to its strictly collimated nature.
Scattering is a phenomena that happens when an optical beam and scatterer, such as an air or water particle, collide. Scattering is wavelength-dependent and the energy of a scattered optical beam is not changed (assuming no absorption); only the directional redistribution of optical energy occurs, leading to a reduction in the intensity of the beam over a longer distance. Atmospheric scattering is divided into three types:
- Rayleigh scattering (molecule scattering): occurs when a scattering molecule is smaller than the wavelength of incident light.
- Mie scattering (aerosol scattering): occurs when a scattering molecule is larger than the wavelength of incident light.
- Non-selective scattering (geometric scattering): occurs when a scattering molecule is much larger than the wavelength of incident light. This phenomenon is unique from the previous two in that it scatters all wavelengths of electromagnetic radiation equally-that is, non-selective scattering is not wavelength dependent.