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Abstract Recent research highlights the abundance of floccule (flocs) in rivers, formed by aggregation of clay particles with organic matter. These flocs affect the transport and the eventual fate of clay. Flocs exhibit distinct behaviour from the unflocculated sedimentary counterparts: they can deform and break, and have higher settling velocities, which may in turn cause flocs to deposit and possibly interact with the riverbed. Here, we conducted systematic experiments in a laboratory flume to identify the mechanisms by which flocs and bedforms interact. Flocs showed a saltating (bouncing) behaviour, and were incorporated in the sediment bed as single flocs, clusters, or strings, via deposition and burial in the lee of a dune. Dune geometry was negligibly impacted by the presence of flocs. In natural systems, the burial of flocculated clay particles can affect contaminant spreading, aquatic ecology, the interpretation of deposition patterns, and clay transport.