The current study aims to evaluate concentrations of trace elements (Pb, Cd, Fe, Co, Mn, and Ni) in collected water samples, particulate sediment, and benthic fauna at four stations along the Tigris River in Baghdad, Iraq. Physa gyrina, Corbicula fluminea, and Oligochaetes are regarded as pollution indicators, and their contents in trace elements are determined. Four sampling stations were selected while considering the multiple sources of water pollution. The lowest trace element concentrations were observed in the water compared to the sediment and particulate phases. Specifically, cadmium levels in the dissolved water at stations 3 and 4 exceed the WHO limit attributable to the unrestricted discharge of industrial effluent and sewage directly into aquatic systems. At the same time, Ni has the lowest level among benthic species, while Pb and Fe have greater levels. Wastewater from neighboring hospitals and the region’s power plant is responsible for the contamination with trace elements in water (Mn, Pb, Co, Fe, and Cd) and sediment (Pb, Cd, and Mn). Furthermore, the biological sedimentation factor (BSF) of trace elements in benthic organisms ranges between 0.2 and 59.14 in all organisms as follows: Pb>Cd>Co>Ni>Fe>Mn. Oligochaetes have the greatest capacity to accumulate trace elements compared to Physa gyrina and Corbicula fluminea. Interestingly, the study confirms high contamination levels of trace elements at the sampled stations, notably Pb and Cd, which highlights the urgent need for intervention to mitigate the sources of pollution on the banks of the Tigris River.