Abstract—In comparison with Radio Frequency (RF), the Free Space Optical Communication (FSOC) provides higher bandwidth, free license operation, and less initial expenditure. However, its susceptibility to changes in atmospheric weather conditions. In this paper, the impact of irradiance fluctuation on FSO systems was estimated using Rytov theory for major cities in South Africa. The extent to which the refractive index structure parameter, propagation distance and link margin affect the optical signal power at the receiver is discussed and the different methods used in evaluating the atmospheric turbulence effect are investigated. In order to achieve the stated aim, meteorological data, altitude, visibility, and wind speed were obtained from the archive of South Africa Weather Services for a period of 3years (2016-2018) over seven locations which include Cape Town, Pretoria, Upington, Bloemfontein, Emalahleni, Polokwane, East London. Results show that Emalahleni was found to possess the poor visibility of 4.4 km because of foggy conditions due to the activities of miners and other environmental factors, followed by East London with average visibility of 4.8 km. From the analysis of link margin, it was shown that FSO link attenuation reduces at higher wavelengths and long link distances due to the effect of geometric and atmospheric losses. The results show that the rate of decrease in link margin is much higher in the inland regions as compared to the coastal regions; therefore, FSO systems are prone to outage during high rainfall and longer range of connections.