Observations of the lower Mississippi River channel in 1999–2003 with side-scan and subbottom seismic profilers, multibeam bathymetry, core radiotracers (7Be, 137Cs, 210Pb, and 234Th), and water-column profiles of fluid and suspended sediment properties are utilized to constrain the timing, location, and intensity of the seasonal storage of fine-grained sediments in the estuarine channel reach below Venice, Louisiana. Unlike earlier studies that suggested little or no estuarine sedimentation was taking place in the river, the present study demonstrates that the river channel above the Head of Passes seasonally stores as much as 10% of the annual suspended sediment discharge during periods of falling-to-low Mississippi water discharge associated with salt stratification in the channel thalweg. Mud deposits are up to 3.2 m thick with 7Be-derived sediment deposition rates of up to 8.9 mm/day. Water-column profiling and 234Th/7Be ratios suggest that (1) particles are transported and settled mainly as flocs; and (2) riverine flocs are settling through the strong salt-wedge halocline and are protected from re-erosion by the salt stratification. With onset of the spring freshet and the corresponding seaward retreat of the saltwater wedge, the entire volume of fine-grained material stored in the lower river (except in low freshet years) is remobilized and transported to the Gulf of Mexico in the turbid freshwater plume. This tidal hysteresis strongly influences the timing of sediment supply to the ocean: high turbidities in the shelf plume during rising water discharge spikes of 1- to 2-week duration are the product of local channel floor remobilization as well as increased supply from the drainage basin. Pulsed resupply of sediments and the pore-water products of early diagenesis potentially have major implications for issues such as continental margin carbon budgets and coastal eutrophication. Companion surveys conducted in the lowermost 12 km reach of the Atchafalaya distributary of the Mississippi show no evidence of saltwater wedge intrusion at low discharge or seasonal fine-grained sediment storage, likely due to the shallow (7 m) river-mouth sill that impedes the upstream movement of Gulf water.