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Zahedan City is situated in the Sistan basin, a highly active dust source region that poses significant risks to human and ecological health due to potentially toxic elements (PTEs) present in atmospheric dust. In this study, we investigated the concentration, sources, and human health risk assessment of PTEs in 88 monthly atmospheric dust samples collected between December 2020 and October 2021 using inductively coupled plasma mass spectrometry. The results showed that the concentrations of PTEs in atmospheric dust followed the descending order of Mn > Zn > Ba > Sr > Cr > V > Ni > Cu > Pb > Co > As > Mo > Cd. The calculated enrichment factors revealed significant enrichment for As > Zn, moderate enrichment Pb > Ni, deficiency to minimal enrichment for Cr > Mn > Fe > Sr > Cd > V > Cu > Ba > Co, and no enrichment for Mo. Arsenic was found to be the major contributor to the potential ecological risk index, accounting for 55% of the total risk. The widespread utilization of arsenic-based pesticides in the surrounding agricultural lands may be a significant contributor to the severe arsenic pollution in the region. The winter season exhibited the highest monthly mean concentrations of Zn and Pb possibly due to temperature inversions trapping local anthropogenic pollutants near the Earth's surface. Cluster analysis revealed a strong correlation between Ni-Cr-Fe-V-Mn-Al, which shows mainly the geogenic source for these elements. The predominant exposure route for non-carcinogenic risk to humans was ingestion. The hazard index (HI) values for the heavy metals studied decreased in the following order: Cr > As > Pb > Ni > Zn > Cu > Cd, for both children and adults. The HI values indicated that there was no possible non-carcinogenic risk associated with exposure to these heavy metals in Zahedan's atmospheric dust. The result of the inhalation cancer risk assessment suggested that while the potential risks of cancer for As, Cd, Cr, and Ni were below the safe level, the levels of Chromium were close enough to the threshold to warrant further investigation and monitoring., (© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)