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 VR=2.44, temperature difference between the two streams ΔT=4.70 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 VR. The MI contained only co-rotating 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 3D 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.