Beni river is an important tributary in the Amazon basin. There, the Bolivian government decided the construction of a two-dam cascade hydropower system, including Chepete dam and El Bala run-of-the-river dam. The main concern is the high sediment transport in Beni river. Then, the aim of the research is the application of Delft3D model to estimate the influence of El Bala run-of-the-river dam on the sediment transport and morphological activity of Beni river. The model was calibrated for natural conditions based on ADCP data and sediment transport measurements collected from the river. The implemented model was able to reproduce hydrodynamics and sediment transport in natural conditions. Hence, several scenarios were tested. A hydrodynamic and morphological model was set to test the influence of the dam on the river for hydrodynamics, sedimentation and erosion processes in Beni river. Results show that Delft3D performed very well in modelling sedimentation and erosion processes in Beni river, the model was able to predict the expected erosion process due to the presence of Chepete dam, upstream of El Bala, which retains the sediment load of Beni river affecting the morpho-dynamics of the river. Additionally, the model was able to predict a sedimentation in the reservoir.