Accelerated soil erosion in Iran causes on-site and off-site effects and identifying of sediment sources and determination of their contribution in sediment yield is necessary for effective sediment control strategies in river basin. In spite of increasing sediment fingerprinting studies uncertainty associated with magnetic susceptibility properties has not been fully incorporated in models yet. The objective of this study is determination of the relative contribution of sediment sources using magnetic susceptibility properties (High frequency, Low frequency and Frequency dependence) incorporated in uncertainty mixing model. For this purpose, 25 bed sediment samples were collected from the outlet of drainage basin and outlet of sub-basins and their magnetic susceptibility was measured and calculated. The results of Kruskal–Wallis test and discriminant function analysis showed that magnetic susceptibility properties can be used as optimum set of tracers in the uncertainty mixing model. The results of Bayesian mixing model indicated that mean (uncertainty range) relative contribution of Sparan, Joyband and Boyoukchay are 92 (83.9-94.8), 2.8 (0.2-10.7), 5.7 (0.2- 10.5) percent, respectively. According to these results, the highest amount of sediment yield is related to Sparan sub-basin and these results could be used in soil conservation and management planning.