This paper describes a theoretical, hydrodynamic model and represents the critical parametric uncertainties associated within the model. The mathematical model structure has been constructed by using process-based equations including both mechanistic and empirical relationships regarding the bedload and suspended sediment transport rate. Model equations are used in bed elevation determination due to the accumulated sediment load within the channels. According to the model, simulations of sediment concentration profiles are in agreement with typical depth averaged sediment profile graphs. Simulation results suggest that total sediment concentration is higher near the river bed than closer to the surface and bedload concentration begins to increase linearly with increasing depth while suspended load tend to decrease. Sediment transporting capacity is found to be higher in stream links with higher velocity and slope values. Results also indicate that bed elevations can change considerably according to changing flow conditions. A Generalized Sensitivity Analysis procedure is applied to the model to determine the correlation between the system’s components and the most significant parameters. Results of the analysis suggest that five out of seven parameters, including sediment density, porosity, river depth, channel slope and river flow, are significant at the 90% confidence level or greater. These parameters contain a low level of uncertainty, because they showed much less correlation with the other parameters.