The performance of free space optical communication (FSOC) systems is severely degraded by certain atmospheric conditions prevalent in places where they are deployed, in spite of their numerous advantages. In clear weather conditions, the random fluctuation in the atmosphere’s refractive index causes substantial scintillation losses to transmitted optical signals. It is therefore imperative to estimate the potential losses due to atmospheric turbulence in locations where FSOC links are to be deployed. This will provide the necessary fade margin for FSOC systems so that designed links withstand such atmospheric disturbances. In this paper, statistical analysis of wind speed data collected for various cities of South Africa is used for calculating the corresponding refractive index structure parameter (${{\displaystyle C}}_n^2$). These ${{\displaystyle C}}_n^2$ values, as well as the zero inner scale and infinite outer scale model and finite inner and finite outer scale model, are used in computing the scintillation indices not exceeding 50%, 99%, 99.9%, and 99.99% of the time for the investigated locations. The Lognormal and Gamma–gamma distribution models are then employed for the computational analysis of the irradiance fluctuations and channel characteristics while considering the effect of pointing errors for weak and moderate to strong turbulence regimes. Finally, derived mathematical expressions for outage probabilities and bit error rate (BER) performances for FSOC links, employing various intensity modulation and direct detection (IM/DD) schemes, are presented.