AbstractDiagenetic processes in anoxic sedimentary environments influence sediment magnetic properties mainly through dissolution of detrital magnetite and precipitation of authigenic greigite. Recently exposed late Holocene Dead Sea sediments provide an opportunity to study the processes governing greigite formation and preservation, and their relation to different hydrological settings. Magnetic data and pore‐fluid compositions were obtained from three Holocene sections along a N‐S transect on the western Dead Sea shore: Og, Ein‐Feshkha (EF), and Ein‐Gedi. The northern sections are closer to the major freshwater source to the Dead Sea‐the Jordan River. Detrital titanomagnetite is present at all sections, but greigite is the dominant magnetic phase at Og and EF. Bulk rock magnetic data vary between and within the sections by over 3 orders of magnitude, where higher values indicate higher greigite concentrations. At the three sites, pore fluids have similar or lower salinity than the modern and Holocene Dead Sea brine, with variable and dissolved iron (Fe2+) and sulfate (SO42−). Magnetic property changes are reflected by iron and/or sulfate microbial reduction that controlled sedimentary greigite formation. We propose that the N‐S greigite decrease suggests that anoxic microbial activity was controlled by labile organic matter and/or reactive iron brought by, or formed as a result of, freshwater influx from the Jordan River. Hence, greigite concentration changes depended on past freshwater input to the hypersaline lake and proximity to the freshwater source. The apparent relationship between hydrological conditions and magnetic properties provides a new method to trace past hydrological changes in the Dead Sea.