Remarkable 3D flow structures occur at river confluences with small density differences due to differences in sediment concentration or temperature. We explain these by comparing numerical simulations for an idealized confluence with aerial photographs of several river confluences where color differences express the pattern of density differences at the surface. We analyzed numerical simulations of the Rio Negro–Solimões confluence near Manaus, Brazil, in more detail. The numerical model of the idealized confluence showed that the dense water flowed under the light water and the light water over the dense water in a spiraling motion, distorting the interface between the two waters. The horizontal part of this interface moves upwards in downstream direction. Constraining of the spiraling motion in a narrow river downstream of the confluence can cause local up- and downwelling near the banks. A mixing layer can develop when the flow velocities of the two tributaries differ, but strong spiraling motion due to the density differences can suppress this development. The aerial photographs and all numerical simulations showed similar density patterns at the water surface. Even small density differences can have a significant impact and hence need to be considered when analyzing and modeling 3D flow at confluences.