In the presented paper the analysis of uncertainty in assessment of annual sediment inflows to the Stare Miasto reservoir is presented. The reservoir is chosen because of its specific structure. It is two-stage reservoir. The upper part of the reservoir is separated from the main part by small upper dam with sluice gate. Upper part is smaller and plays a role of so called pre-dam reservoir designed to collect sediments. In this part the conditions for deposition of sediments are very good, what prevents from sedimentation of the main part. In the research the several data are used. These include reservoir bathymetry, hydraulic structures documentation, hydrologic data and water heads in the main dam. In the analyses the empirical formulae for sediment transport are implemented. The formulae used are Ackersa-White, MPM, van Rijn, Engelund-Hansen, Yang, Toffalet and WilcockCrow. The computations are verified on the basis of current bathymetry measurements and estimated real sediment deposition. The obtained results vary significantly, what indicated importance of the structural uncertainty in analysis of reservoir sedimentation.