Free Space Optical (FSO) communication systems offer high-speed data transfer and secure connectivity, making them suitable for various applications. However , severe weather, especially in desert environments like duststorms and fogs, can significantly impact their efficiency. This paper analyzes the performance of FSO communication systems in desert environments, focusing on the interaction between FSO technology and challenging atmospheric conditions like duststorms and fogs. The research aims to enhance the design and operation of FSO communication systems in these environments, where reliable connections are critical. The study explores various modulation techniques (AM, Duobinary RZ, Modified Duobinary RZ, RZ, and NRZ) to mitigate weather-induced attenuation under duststorm and fog conditions. Real-time visibility data from the meteorological department and Optisystem software were used to estimate attenuation under duststorm and fog conditions in Qassim, Saudi Arabia. The study found that the duo-binary RZ modulation technique offers better performance parameters for maximum link distance, a better Q-factor value, a lower bit error rate, and better received optical power at 25 dB/km attenuation.