The hydrodynamic processes in large river–lake systems and their responses to flow regulation represent regionally unique and highly significant issues. This study presents the implementation, validation and application of a two-dimensional hydrodynamic model to a system comprising a section of the Huai River and Hongze Lake, China. The validated model enabled the identification of hydrodynamic characteristics by analysing the flow patterns under the influence of the local flow regulation. Effective flow regulation measures during flood period reduced the retention time of floodwater in the lake and contributed to a low-velocity current field in the northern part of the river–lake system. Throughout the non-flood period, a distinctive flow pattern emerged due to persistent easterly winds, resulting in a dual circulation pattern in the interconnected region between the northern and central segments of the system. The investigation of flow patterns revealed the creation of stagnant water zones in the northern sector of Hongze Lake. Distributing a substantial portion of outflow discharge to the Erhezha gate could lead to an expansion of the flood passing area by scenario analysis. Simultaneously, implementing intermittent control over the Erhezha gate drainage effectively heightened the current velocities in the stagnant water zone. The deliberate allocation of outflow discharge has a substantial impact on the flow dynamics within a vast river–lake system during the flood season, which carries significant research potential in enhancing the local water self-purification capacity and water quality.