This study investigates the biogeochemical composition of the atmosphere in the southern regions of Uzbekistan (Surkhondarya and Kashkadarya regions). The research identifies the natural and anthropogenic sources of air pollutants, characterises the physicochemical composition of dust–aerosol particles (PM₂.₅ and PM₁₀), and demonstrates their significance within an integrated environmental monitoring system. Seasonal sampling campaigns were conducted at five monitoring sites from 2023 to 2024. Atomic absorption spectrometry (AAS) and inductively coupled plasma–optical emission spectrometry (ICP-OES) were employed to quantify heavy metal concentrations, while ion chromatography determined major anion and cation profiles. Biogeochemical indices (Igeo, PI, ERI) were computed for each site, and spatial distribution was mapped using GIS. Results indicate that PM₂.₅ and PM₁₀ concentrations exceed WHO guideline values by 3–7-fold during summer, with heavy metals Fe, Mn, Pb, Zn, and Cu showing marked seasonal peaks. Source apportionment attributes 52% of PM₁₀ to soil erosion and dust storms, 21% to industrial emissions, and 14% to transport. Ecological risk assessment classified two sites in Surkhondarya Valley as 'moderately hazardous' and one as 'highly hazardous'. Integration of biogeochemical analysis into routine monitoring is scientifically substantiated and recommended.