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In this paper, sediment deposition and trapping efficiency in shallow rectangular reservoirs were numerically estimated considering secondary flows. In order to do this, three dimensional (3D) steady, incompressible, Reynolds-averaged Navier-Stokes (RANS) equations with the standard k-ε turbulence model were used as the goving equations. The drift-flux model also was used to model the solid phase. In the next step, the developed model was validated using the available data. Then it was used to simulate the sediment deposition and trapping efficiency in shallow rectangular reservoirs, considering secondary flows. The results show the sediment is trapped in the inlet cer of the reservoir, and two pairs of large vortices on the sides and two pairs of small vortices at the inlet cer of the reservoir are observed. Finally, the effects of the input angle of the reservoir to the trapping efficiency are evaluated and the results are discussed.