Sand storms and fine dust are known as the most important atmospheric problems in many windy regions around the world, especially in arid and semi-arid areas. Besides all the obvious negative effects of fine dust on human life, this phenomenon can extremely reduce the physical and chemical quality of output water from treatment plants into the distribution systems. In order to show and evaluate the impact of fine dust on the physico-chemical quality of the water, a long-term (three years: 2017–2020) experimental investigation was done in the Sistan region (Iran) which is one of the most popular regions in the world with high amount of annual fine dust level. The final results showed that the most physical and chemical quality indices of output water from the local treatment plants became progressively worse after the fine dust process. The total dissolved solids (TDS) and turbidity of the water, which could even obviously be seen in the samples, were increased so that the TDS level was raised to more than 850 ppm. The level of some metals such as Fe, Ca, Mg, Na, and K increased significantly but stood within the standard levels. pH level was increased to up to 8.3 in some water samples. In addition, high levels of NO3, SO4, F, EC, HCO3, Cl, CO3, and PO4 were observed in all water samples after fine dust processes. Also, the t-student analysis showed that there was a high correlation between wind speeds and the reduction of physical and chemical quality indices in most of the water samples. Finally, the experimental analysis showed that most of these chemical elements originated from the vast bed (5,660 km2) of the dried-up Hamun’s Lake where the winds were blown over.