Throughout Iraqi rivers, extensive depositional processes have led to the accumulation of significant minerals that threaten aquatic life due to geochemical recycling and the repeated resuspension of particles from the benthic habitat into the water column. These minerals can enter the food chain through residue consumption. This study evaluated the impact of certain elements in river sediments using field investigations and contamination indices, including the contamination factor (CF), geo-accumulation index (Igeo), enrichment factor (EF), and pollution load index (PLI), followed by statistical analyses. All indices indicate, to varying degrees, severe mineral contamination in the study area. Sediment samples were systematically collected from agricultural zones, river bends and islands, urban areas, and sites upstream and downstream of the Al Hindiyah barrage. The results demonstrate that surface sediments are contaminated with specific minerals—particularly Cd, Cu, Ni, Co, Fe, Mn, and Cr—exceeding the sediment quality guidelines established by the USEPA. The enrichment factor (EF) analysis indicates very high enrichment of Cr, extremely high enrichment of Cd and Cu, significant enrichment of Ni, Zn, and Co, and moderate enrichment of Mn across the studied sites. The contamination factor (CF) index reveals moderate contamination levels for Pb, Cu, Co, and Cr, while Cd exhibits a very high contamination level. According to the Igeo index, the studied sites are moderately to strongly polluted by Cd and moderately contaminated by Cr and Cu. Based on the Pollution Load Index (PLI) for site quality assessment, all sampling sites are classified as unpolluted, except for the site on Um Shuhiaba Island, where baseline levels of certain elements are elevated. Principal Component Analysis (PCA) and Factor Analysis (FA) demonstrate that all elements are well represented, accounting for a cumulative total variance of 72.76%. A comprehensive investigation of surface sediment contamination indicates that the sediments pose a hazardous risk to the environment, with emissions primarily originating from anthropogenic sources. This is particularly concerning given the extensive use of the upstream area for drinking water, agriculture, and livestock. Therefore, variations or even opposing effects of environmental management practices on mineral conditions must be carefully considered when assessing the ecological impacts of riverbank management.