Mud particles comprise the vast majority of riverine sediment discharges and mediate the transfer of particulate organic carbon from terrestrial landscapes to deltas. Historically, mud particles were considered washload – sediment that may travel hundreds of kilometers without depositing, implying that rivers are fast paths through which mud-associated organic carbon exits terrestrial landscapes. However, recent studies have found that the interaction of particulate organic carbon and mud particles promotes flocculation, which enhances settling velocities, potentially driving mud and carbon deposition into the riverbed, point bars, and overbank deposits. Here, we study the transport of mud, developing and calibrating a statistical model based on particle hop lengths and transient storage residence times to investigate these processes for the Yukon River Basin, which has a carbon-rich, sub-arctic floodplain. From our field observations, we find that flocculated mud settles at about 2.86 mm s<sup>-1</sup> and constitutes about 10 % of the sediment in the active layer of the riverbed, 20 % of the sediment in point bars, and 60 % of the sediment in overbank deposits. Our model shows that 60–80 % of mud particles transit the alluvial reaches of the Yukon River over decades, rather than the few weeks predicted if mud was a passive water tracer. Nearly all (~99.9 %) of the decadal transit time is spent in the active layer of the riverbed, as opposed to the water column. 20–40 % of mud particles enter floodplain storage during alluvial transit, extending their transit time from decades to centuries, or even millennia. Individual riverbed depositional events only last a few days because of rapid water column entrainment, whereas individual floodplain depositional events typically last centuries or longer, highlighting the dynamic nature of the riverbed. Consequently, transient storage in river deposits may allow substantial carbon dioxide and methane generation in rivers.