Patterns of sediment transport to the Dead Sea basin during late Pleistocene and Holocene times were evaluated by comparing previously established lake levels with patterns of transgressions and regressions in fan deltas at the lake margins. While the lake-level history reflects the hydrological regime in the drainage basin, the transgression–regression patterns reflect the response of the clastic sediment transport to the regional hydrology and morphology of the basin. By using the two techniques we are able to demonstrate the time relationship between the factors controlling the deposition. Six sequences are exposed at the western margins of the basin. Their chronology was obtained by U–Th, radiocarbon, and luminescence ages on aragonite and quartz sand from the Samra, Lisan, and Ze’elim formations, which cover the past ~ 160 ka. Our data shows a lag between periods of high water inflow and clastic sediment flux to the basin. During highstands the sediments were stored in deep (100–200 m), long estuaries that formed in incised canyons into the east and west bounding escarpments. During lake-level falls the stored sediments were flushed out, forming prograding lowstand fan deltas. This leads to a high sediment flux during early stages of arid conditions following extreme high lake levels.