Water draining from heavily industrialized basins introduces significant amounts of pollutants to the rivers water and sediments. Heavy industrial activities in the Shatt Al-Arab basin result in increased pollutant loads to the river's surface sediments. Therefore, it becomes crucial to investigate the influence of anthropogenic activities on both spatial and temporal scales. This study unfolded the extent, sources, and distributions of heavy metals pollution in the sediments of the Shatt Al-Arab River. Extensive samplings were performed during the dry and the wet seasons at 25 stations along the river course for the analysis of 11 heavy metals. The analysis revealed high pollution levels in the river sediments compared to both their historical values and international standards. Statistical analysis techniques such as Principal Component Analysis (PCA) and Factor Analysis (FA) were applied. Statistical analysis showed that all the elements were well represented by four varifactors that explained a cumulative total variance of 74%. PCA/FA indicated that most investigated metals were of anthropogenic origins (i.e., industrial, residential, and agricultural sources). Pollution indices that were applied, such as Contamination Factor (CF) and Nemerow Pollution index (PN), indicated that sediments were: (i) considerably contaminated with Fe and Mo (ii) moderately contaminated with Cr, Zn, Ni, Cu, Pb and Mn and (iii) not contaminated with Co and V. The PN values indicated serious pollution in the river sediments in all sites, even though the pollution was not evenly distributed, i.e., the upstream reaches of the river were more polluted compared to the downstream parts. In contrast to many studies that have reported changes in heavy metals concentrations due to seasonal variations, our data showed no significant relationship between metals concentrations and seasonality. This study addresses several of the major limitations of the current knowledge on this river's pollution sources and analysis, such as the limited number of analyzed pollutants and restricted samplings in the current literature. The findings necessitate the implementation of effective management strategies to control pollution in the river basin.