Monitoring the pollution status of freshwater resources is an important step in sustainable planning. This study aimed to determine the distribution and sources of metals in the sediments of the transboundary eastern Anatolian/Caucasus region Kura river as well as its ecological risk level. Surface sediment samples were collected from eight sites along the human disturbance gradient. Multi-element analyses of the collected samples were performed using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Chlorophyll degradation product (CDP) analysis was performed spectrophotometrically. OC analysis was carried out using the titration method. The data obtained were evaluated using the indices of enrichment factor, geo-accumulation, modified hazard quotient and ecological contamination index and potential ecological risk. The average content of metals in the sediment at the eight sites was of the following descending order from highest to lowest: Al > Mn > Zn > V> Ni > Cr > Cu > Co > Pb > As > Cd > Tl > Hg. According to the distribution of raw metal values, urbanization is not the only factor controlling metal distribution. Adsorption processes and organic material content also emerge as an important factor. Enrichment factor values were of the following order: T1 > Pb > Mn > Hg > Cr > Co > Cd > Ni > As > Zn > Al > Cu > V. Results revealed that the sources of Cu, V and Al were lithogenic, in contrast to Tl, Pb, Mn, Hg, Cr, Co, Cd, Ni, and As, thus pointing to human-induced accumulation. According to the potential ecological risk index, these elements have the potential to create medium-to-high level ecological risks and were substantially of atmospheric origin. The ecological contamination index is also consistent with these findings in terms of risk level. A municipal waste stream, fossil fuel burning and a cement plant operating in close proximity also appeared to be the possible sources.