The construction of gates in watercourses could change the original hydrological and hydrodynamic processes of drainage basins, eventually having a widespread cumulative influence on river habitat and fish resources. In this study, the hydrodynamic force in the Yongjiang River basin, China, was calculated using the MIKE FLOOD model, including water depth and flow velocity. Subsequently, the habitat conditions suitable for yellowcheek carp were used to analyse ecologically suitable flow for this target species during the spawning period at the main spawning site (Fenghua River). Different schemes of simultaneous operation of the dam gates on the Fenghua and Yaojiang rivers were simulated after gate construction on the Yongjiang River estuary, and their influence on fish spawning and migration in the main stream was investigated. During the fish spawning period, the ecological flow for facilitating yellowcheek carp spawning in the Fenghua River was 160 m³/s. The discharged water flow of gates increased to 90 and 250 m³/s, respectively, in the tributaries of the Yaojiang and Yongjiang rivers, causing the average flow velocity of the target watercourse to increase by 0.2 m/s. Based on our results, we provide recommendations for regulating water flow to enhance ecological watershed planning after gate construction along watercourses.