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The effects of temperature induced stratification on flow hydrodynamics, thermal mixing, and the capacity of the flow to entrain sediment at a medium-size stream confluence with a highly discordant bed are investigated. To isolate the effects due to differences in the temperature/density of the incoming streams, two simulations were conducted with identical flow conditions (mean velocity ratio = 0.41 and temperature difference between the two streams Delta T = 4.7 degrees C). In the first case the Richardson number was Ri = 0 (no coupling between the temperature and the momentum equations via the Boussinesq approximation), while in the second simulation Ri = 0.67. Even in the Ri = 0 case the structure of the mixing interface (MI) was different from the one expected for concordant bed confluences with a similar confluence angle and velocity ratio. The MI contained only corotating eddies shed in the shear layer forming on the fast-speed side of the confluence apex. In the Ri = 0.67 case no wake region was present but a large recirculation eddy formed not far from the confluence apex. In both cases, the flow near the upstream part of the MI was found to be highly 3-D and to allow the passage of particles from one side of the confluence to the other. While in the Ri = 0 case mixing was driven by the MI eddies, in the Ri = 0.67 case mixing was controlled by large near-bed intrusions of heavier fluid from the tributary containing colder water and also by the fluid advected in and out of the recirculation eddy.