Confluence exists widely in natural rivers where sediment, pollutants, and fish are prone to confluence, and studying flow structure can provide guidance for studying the evolution of riverbed and improving river environmental health. In the current study, numerical study, employing the renormalization group (RNG) k-ε turbulence model, was carried out after comparing three different turbulence models. Subsequently, the structure and development of secondary flows and separation zone is analysed by changing the morphology of incoming tributaries, such as straight channel or bend. The results show that a separation zone with low velocity and pressure, but high turbulence is formed downstream of the junction while two secondary flows form on the sides of the shear plane downstream. The shapes of the separation zone and secondary flow at the confluence are defined in a new way.  The secondary flow formation process is reversed within the separation zone and highly complicated for the various confluence hydraulic conditions. This work can provide scientific basis for improving the riverbed morphology and aquatic animal ecology of natural river by using confluence estuary.