The Gediz River, which flows through many cities and connects to the Aegean Sea, has an important economic potential for the Aegean Region. Given this importance, a detailed assessment of potential toxic elements (PTEs) in the river sediment is required. 18 PTEs (Co, Cr, Cu, Mn, Ni, Fe, Al, Se, Mo, Sr, Mg, Ag, Pb, Zn, As, Hg and Cd) were collected from 13 stations along the Gediz River covering three basins to determine the level of pollution and ecological risk. For pollution assessment in sediments, contamination factor (CF), pollution load index (PLI), geographical accumulation index (Igeo), enrichment factor (EF) were analyzed. Potential impacts of PTEs in the sediment matrix of the Gediz River on human health (Potentatial Ecological risk factor (Eir), Potentatial ecological risk index (PERI), hazard quotient (HQ), hazard index (HI), lifetime cancer risk (LCR) were investigated in detail. The mean concentrations of the majority of the PTEs exceeded the corresponding background values, indicating that the highest pollution load was in the downstream basin. Based on the PTEs spatial distributions and pollution indices, the Gediz River was found to have high accumulation of As, Cu, Cr, Ni and Zn in the sediments. In addition, HQing and HI values were greater than 1 for As, Co, Cr, Mn, Ni and Pb in all three basins. It was determined that As and Cr had a high effect in terms of LCR value. Correlation analysis and principal component analysis were also applied to explain the main sources of PTEs formation.