Flow field in shallow waters, which is characterized by its complex mixing process and inherent dynamic nature, is interesting mainly due to its practical importance (e. g. in free flushing operation and sedimentation in large reservoirs). 3D numerical models make it possible to track two-dimensional large turbulence coherent structures, which are the dominant phenomenon in shallow reservoirs flow field. In the present study a fully three-dimensional numerical model SSIIM that employs the Finite Volume Approach (FVM) was utilized to reproduce the 3D flow field. Various shallow reservoir geometries with fixed and deformed equilibrium bed were considered. The measurements by Large-Scale Particle Image Velocimetry techniques (LSPIV) and Ultrasonic Doppler Velocity Profiler (UVP) over the flow depth were used for model validation. Outcomes revealed reasonable agreement between the simulated and measured flow velocity field even when an asymmetric flow pattern exists in the reservoir. © 2014 Taylor & Francis Group, London.