A three-dimensional (3D) numerical model was developed to investigate the thermodynamic and sediment processes in a subtropical drinking water reservoir. Data-driven models were also established to generate the inflow conditions. The modelling outputs revealed that climatic forces such as storms and winds significantly impact lake stratification and mixing processes. The sediment transport is driven by storm events, during which sediment delivery to the reservoir is dominated by allochthonous flux. The sediments are transported from riverine zones to transition zones and finally to lacustrine zones. It is estimated that sediment accumulation could have reached 100,000 kg during the largest storm event in February 2015. The winds can lead to a strong vertical water cycle, especially at the centre of the reservoir, and strong winds result in bed erosion in shallow regions. The outcomes of this paper benefit future research by providing a modelling approach for understanding the hydrodynamics of lakes and reservoirs under a variable climate, and also the local water utility by providing insights for an improved management of the reservoir of this study.