Single-medium thermal energy storage is widely used for heat and cooling supply. During the charging and discharging process via jet nozzles, strong transient turbulent mixing and heat transfer occurs. Hence, qualitative and quantitative understanding on the thermal mixing mechanisms are beneficial to the design and operation of the thermal storage system. In this study, we perform large eddy simulation (LES) of a three-dimensional stratified water storage tank with a single jet issuing hot water to study the long-time behaviour. The simulation data are utilised to investigate the flow and thermal characteristics of the tank, especially the formation of the buoyant jet and the thermal dispersion along the vertical direction. It is shown that the fine vortical jet shear-layer structures are responsible for most of the turbulence mixing. Furthermore, the LES results are regarded as reference data for assessing the flow predictions that result from different solver set-ups and turbulence models employed in unsteady Reynolds averaged Navier–Stokes (URANS) calculations. The results demonstrate that the realisable model can yield satisfactory predictive accuracy, once the buoyant production is correctly included in both transport equations. Finally, we examine the effect of different choices of turbulence heat flux models, including the standard/generalised gradient diffusion hypothesis (SGDH and GGDH) and algebraic heat flux model (AFM), on the numerical predictions. The results indicate that the URANS with GGDH and AFM can accurately and efficiently predict the flow and thermal fields in the turbulent flow regime.