CHANNEL confluences have received considerable recent attention in the fields of geomorphology 1-3, sedimentology 4-9 and hydraulic engineering 10-13. Where channels join, rapid changes in fluid velocity, turbulence intensity, channel hydraulic geometry and bed geometry may occur 14-17. Previous models of junction dynamics have tended to assume that the confluent channels are of equal depth 10,18, a condition that may be found only rarely in natural junctions; more often, the depths of confluent channels are different 19. This discordance is commonly the result of the formation, at the mouth of each confluent channel, of bars that possess steep avalanche faces which dip into a central junction scour 1,2,5,20. Here we suggest that when channels of different depth join, the mixing layer that forms at their confluence is distorted by interacting with a separation zone which forms in the lee of the mouth of the shallower channel. This mixing-layer distortion imparts a complex three-dimensional flow to the junction, promoting vertical fluid upwelling and significantly enhancing rapid mixing within the flow of the shallow tributary, while retarding the rate of mixing across the flow of the deeper channel. Suspended sediments or contaminants within the deeper channel may be transferred rapidly across the flow of the shallower tributary, upwelling downstream of the junction.