Introduction: The industrialization of human societies is one of the factors in increasing the injection of pollution into surface waters. Contamination in the river is maintained both in the water stream and in the sediment Bed of the river. The hyporheic zone is the saturation zone of the riverBed, which has a very important function in the transmission of pollution. River Bed-form is one of the effective factors in creating hyporheic exchanges between surface flow and sediment Bed. Transient Storage Model (TSM) is one of the suitable methods in the analysis of advection and dispersion of pollution in rivers with hyporheic zone. The efficiency of the Transient Storage Model (TSM) depends on accurate estimation of the four parameters of the model (Dx, As, A and α ). Previous studies have examined the effect of Bed-form on hyporheic exchanges, but the effect of these exchanges on contamination transmission has not been considered. On the other hand, previous studies have not explored the effect of hyporheic exchanges caused by the formation of the Bed-form on the four parameters of the transient storage model (TSM). In this study, the effect of dune Bed-form on the transmission of pollution was analyzed. The effect of dune formation on the four parameters of the transient storage model (TSM) with a numerical model (OTIS and OTIS-P) and the temporal moment approach (TM) was also discussed. Methodology: Experiments of tracer material (NaCl) were performed in a flume with a length of 12 m, a width of 0. 5 m and a height of 0. 7 m applying four different flow discharges (5, 7. 5, 10 and 12. 5 l/s). The experiments were performed in the range of average flow velocity (U) from 0. 087 to 0. 361 and in the range of Froude number (Fr) from 0. 069 to 0. 290. An ultrasonic flow-meter was used to measure the flow discharge in all experiments. Grain material with an average diameter (D50) of 11. 85 mm and the porosity (n) of 0. 28 were used to create a sedimentary Bed. The first Bed (WF1) with a thickness of 32 cm, a width of 0. 5 m and a length of 10 m was created in the Flume. In order to examine the effect of sediment Bed thickness on contamination transmission, a second Bed (WF2) with a thickness of 8 cm, a width of 0. 5 m and a length of 10 m was also created. In this study, the effect of dune Bed-form on the transmission of contamination was analyzed. by creating three dune Bed-forms (D1, D2 and D3) with different wavelengths (λ ) and different amplitudes (∆ ) in the second Bed (WF2). The length of the flume was divided into three equal reaches. Two sensors were placed to measure the electrical conductivity (EC) of water in each reach aiming to monitor the concentration of contamination. A Pitot tube and an ultrasonic depth-gauge were used to measure the velocity (U) and depth (d) of water flow at each reach, respectively. The laboratory results were simulated by the OTIS-P numerical model and the four parameters of the Transient Storage Model (TSM) were estimated. OTIS-P numerical model estimates the four parameters of the Transient Storage Model (TSM) using the Nonlinear Least Squares (NLS) optimization algorithm and then simulates the breakthrough curves using the Crank-Nicolson implicit finite difference method. The parameters of the transient storage model (TSM) were estimated by optimizing the temporal moment approach (TM) relations using the Genetic Algorithm (GA) method and the breakthrough curves were reproduced using these parameters in OTIS software. Results and Discussion: The results showed that increase the thickness of the sediment Bed reduces the longitudinal dispersion coefficient (Dx). Hyporheic exchanges decrease with increasing db/d, so the amount of hyporheic exchanges in WF2 Bed is more than WF1 Bed. Increasing hyporheic exchanges in the WF2 Bed-form reduces the amount of contamination concentration in the main flow area, so the amount of longitudinal dispersion coefficient (Dx) in this Bed-form increases. The results showed that increasing Froude number (Fr) increases the longitudinal dispersion coefficient (Dx) in both cases of Bed thickness. The results showed that the storage zone exchange coefficient (α ) in WF2 Bed was higher than WF1 Bed. Decreasing db/d increases the hyporheic exchanges at the time scale (tf ∗ ), so the residence time of contamination in the sediment Bed increases. Since the storage zone exchange coefficient (α ) indicates the amount of time exchanges of contamination in hyporheic zone, so reducing the Bed thickness (db) increases this parameter. The main channel area (A) considering the D2 Bed-form case was estimated more than that in the D1 Bed-form case. Therefore, increasing the wavelength of the Bed-form (λ ) increases the share of the main flow region area (A) in the contamination transmission. On the other hand, in the case of less exchanges of contamination with the storage zone, the share of the storage zone area (As) decreases with increasing wavelength of the Bed-form (λ ). The results showed that the effect of dune Bed-form on changes in TSM parameters was in the range of Fr <0. 1. Based on the results, that the breakthrough curves simulated using both methods (TM and OTIS-P) are in good fit with the laboratory results. Conclusion: The results of using numerical models showed that increasing db/d causes decreasing the longitudinal dispersion coefficient (Dx) and decreasing the storage zone exchange coefficient (α ). The results also showed that the presence of dune Bed-form increases the main channel area (A) and the storage zone area (As). On the other hand, the presence of dune Bed-form increases hyporheic exchanges, so the amount of changes in the longitudinal dispersion coefficient (Dx) and the storage zone exchange coefficient (α ) depends on the amount of hyporheic exchanges in these conditions. The BTCs simulated by the OTIS-P numerical model and the temporal moment approach (TM) were highly agreement with the laboratory BTCs with the Nash-Sutcliffe index between 0. 89 to 0. 98 and 0. 85 to 0. 98.