Shallow flows can play a significant role in sediment management for dam reservoirs (e.g. sedimentation in shallow reservoirs and free-flow flushing operation). When shallow flow emerges with symmetric or asymmetric patterns, the flow domain exhibits complex three-dimensional (3D) features (e.g. helical flows). This study focuses on the numerical modelling of the velocity field in shallow reservoirs with varying geometries and also varying bed conditions (i.e. flat and misshaped beds). A fully 3D numerical model using the finite-volume method was utilised to reproduce the 3D flow velocity field. The experimentally measured surface velocity in all cases and velocity profiles in one case were used to validate the model. The numerical results showed that a slight disturbance in the inflow boundary condition results in a steady asymmetric flow pattern in reservoirs with a higher defined shape factor, but does not affect the flow pattern in reservoirs with a lower defined shape factor. Nonetheless, the simulated and measured flow velocity fields are reasonably consistent in all cases. These results can be used to optimise the design of sand traps or water storage facilities, and also to optimise sediment management in existing reservoirs.