Consecutive groins and embayment form dead water zones, where sedimentation and congestion of pollutants are often observed. It is thus very important to reveal mass and momentum exchanges between main-channel and side-cavity in river environment and hydraulic engineering. There exists spanwise gradient of streamwise velocity near the junction, and it produces small-scale turbulent vortices owing to shear instability. Furthermore, large-scale horizontal circulations are also generated in the cavity zone. These coherent turbulent structures play significant roles on mass and sediment transfers through a mainstream / embayment boundary. However, the relation between the turbulence and mass transfers is still poorly understood. In the present study, PIV and LIF measurements are conducted in a laboratory flume using a laser light sheets and high-speed CMOS camera, and we compared exchange properties of dye concentration and effects of sedimentation on them among different bed configurations. The both of primary gyre and secondary one are observed in the flat-bed and downward slope conditions, and in contrast, the primary gyre is prevalent in the upward slope condition. It was found that these formations of the horizontal circulations have striking impacts on the mass transfer properties between the mainstream and the side-cavity.