© 2020 The Author(s) Study region: Tarago Reservoir, Victoria, Australia. Study focus: This study investigates the influence of rainfall, river inflow and wind on the temperature stratification of the Tarago Reservoir by incorporating atmospheric and bathymetric conditions using a three-dimensional hydrodynamic model. New hydrological insights for this region: In this study, a three-dimensional (3D) hydrodynamic model was developed and applied to the Tarago Reservoir. The model allowed 3D visualization of the thermal structure, and the seasonal and longitudinal differences in stratification could be quantified using the Schmidt stability index. The simulation results revealed longitudinal differences in thermal structure among the riverine, transition, and lacustrine zones. The bathymetry affects the lake stratification and stability; furthermore, the strong vertical current caused by the sharp bathymetry gradient significantly weakens the stability in deep zones. In addition, this study assessed the impacts of rainfall and wind on lake stability using sensitivity analysis. The results indicated that rainfall decreases the water temperature of the lake but hardly affects the summer stratification. Moreover, the wind not only influences the intensity and duration of stratification but also contributes to the heat storage of waterbodies. The patterns of water current velocities and temperature also showed that the circulation generated by overflow and underflow plumes have a crucial effect on the thermal structure of the transition and lacustrine zones.