Flashfloods entering marine basins can introduce large quantities of terrigenous sediment that deposit on the shallow seafloor. Over time, biological and physical disturbances can induce post-depositional sediment transport to deeper depths. In the hyperarid desert region surrounding Eilat, Israel, flashfloods discharge into the northern Gulf of Eilat-Aqaba, Red Sea episodically. Their deposits may leave useful records of flood events in the marine sediment record. What is poorly understood, however, are the processes of post-depositional alteration of flashflood sediments and the resulting effects on the preservation of the deposits. To address this knowledge gap, short sediment cores (~15–30 cm length, 13 m water depth) were collected at bi/tri-monthly intervals following two different flashflood events in the Gulf of Eilat-Aqaba. Concurrently, mechanisms for resuspension, transport, and vertical mixing of flashflood sediments were investigated by measuring near-bottom water currents and suspended sediment concentrations, photographing demersal fish activities, and measuring the depths and magnitudes of bioturbation using fluorescent sediment tracers. The aim was to record the changing grain size of surface flashflood sediments over time, and identify correlative physical and biological factors. The results show that the original fine-grained flashflood deposits coarsened rapidly following each event. Of the mechanisms recorded, currents generally were too weak to entrain sediment, but did influence the transport of sediment in suspension to deeper depths. Demersal fish resuspended sediment when present, and bioturbation was strongest in the upper 2 cm of the seabed. Despite the rapid reworking of surficial sediments and dissipation of surface flood layers, irregular lenses of fine sediment persisted within the shallow seafloor (down core). Deposition within seafloor holes and depressions, and rapid burial by biologically constructed sediment mounds and ensuing flashflood deposits are proposed as mechanisms for this patchy, localized preservation of flood layers. These findings are useful for identification and interpretation of isolated fine-grained layers in older sedimentary deposits, and for understanding the dynamics influencing the marine sediment stratigraphy in arid, coastal environments.