Hundred-one sediments were collected from Kocacay River and Lake Manyas during a dry season. The concentrations of Pb, Zn, Cu, Mn, As, Ni, Co, V, Mo, Sc, Ni, Bi, Sb, Cr, W, Fe, S, and Al were determined by ICP-AES in the less than 100 pm grain-size fraction. Markedly elevated concentrations (milligrams per kilogram) of some of the metals, Pb (21867), Zn (18635), As (1757), Cd (139), and Cu (632) were recorded. Enrichment factors (EF) of studied elements were determined in the downstream, mine-affected, and non-mine drainage section of the river against average shale and average upper continental crustal (AUCC) abundance. Some elements notably Pb, Cd, Zn, S, Sb, Bi and As show very high EF (e. g. 541 for Pb) in the mine-affected section of the river as compared to the AUCC abundance. These are presumably associated with sulfide minerals such as galena, arsenopyrite, sphalerite, and bismuth found in abundance in the mine-debris piles of Balya Mine. However, high levels of Pb (avg. 1515 mg/kg) are also observed in the non-mine debris drainage section of the river, which shows an EF 124 as compared to AUCC. The result indicates the contribution of metal sulfide bearing lithologic units and element migration via wind from the mine-debris piles. Principal Component Analysis (PCA) was carried out to examine patterns and similarities between concentrations of studied elements. The first component with a high percentage of variance value (51.1 %) explains the dispersion of positively correlated Pb-Zn-Cu-As-Sb-Cd-Mn-S and their association with the mineralogical composition of the mine-debris piles. The second component represents the Ni-Co-Cr association with a low percentage variance (17.2 %) value indicating the contribution of ultrabasic rock units in the downstream section of the river.