Reproductive migration is an essential phase in the life of many fish. During this process, swimming behaviour and gonad development are key factors related to the migration quality, and both factors are strongly influenced by water temperature and flow velocity. Many studies have explored the separate effects of these variables on fish swimming ability or gonad development, but researchers have seldom investigated the simultaneous effects of low flow velocity and water temperature on the fish swimming behaviour and gonad development. To provide that knowledge, we conducted laboratory experiments that explored the coupled effects of low water temperature and flow on warm water fish swimming behaviour and gonad development. At five temperatures (16, 18, 20, 22, and 24 C), we observed the movement of migratory warmwater grass carp (Ctenopharyngodon idellus) at seven flow velocities (0.15, 0.2, 0.25, 0.3, 0.35, 0.40, and 0.45 m/s), then explored their gonad development by comparing the level of plasma 17β-estradiol and testosterone in fish travelling through a simulated fish way (flow stimulation) and in a fish tank (no flow stimulation). We used Bayesian networks to explore the acceptable hydrological condition for fish migration.We found that the minimum flow velocity for acceptable migration quality is a function of the water temperature, and that increasing water temperature improves fish movement success and increases the movement distance, especially at a low flow velocity. In addition, increasing water temperature (between 16 and 24 C in this experiment design) can enhance the effect of flow stimulation on gonad development. Overall, our results can broaden the understanding of reducing water temperature and flow velocity in fish swimming behaviour and gonad development, provide basic data to support hydrological process controls and the development of measures to protect fish migration.