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Surface water quality is largely influenced by both natural processes and anthropogenic inputs. This study involves the characterization of the concentration of heavy metals of Cd, Cr, Cu, Fe, Mn, Ni, Pb, and Zn, and the sources of pollution in water and sediment of the Upper Litani River Basin (ULRB) in Lebanon. The investigation was performed during three seasons of rainy, mid-rainy spring and wet periods for two years during different flow rates. Sediments were characterized by a set of chemical analyses, cation exchange capacity (CEC), mineralogy of the sediments, X-ray diffraction (XRD), and Fourier transformed infrared spectroscopy (FTIR). To assess metal contamination in sediment, Consensus-Based Sediment Quality Guidelines of Wisconsin (CBSQG) were applied. The metals contamination in the sediments was also evaluated by contamination factor (Cf). The test results showed that the effect of seasonal variations was significant in the Upper Litani River Basin. Principal Compound Analysis (PCA) and Pearson's correlation were also performed in this study to compare and determine the correlation between metals in water and sediments. The concentrations of Pb, Cd, Cu, Cr and Zn in all sediment samples are above the norms in winter, while Fe was increased in summer. The results showed that the importance of monitoring of changes of heavy metals values and physico-chemical characterization of different parameters could represent the possibility of a comprehensive assessment of negative pressures on the water and soil ecosystem of Litani River Basin during different seasons.