The Atlantis II Deep is a brine-filled depression on the slowly spreading Red Sea rift axis. It is by far the largest deposit of hydrothermally precipitated metals on the present ocean floor and the only known modern deposit that is analogous to laminated Fe-rich chemical sediments, such as banded iron formation (BIF). The brine pool at the bottom of the Atlantis II Deep creates an environment where most of the hydrothermally sourced elements can be dispersed and deposited over an area of ∼60km2. We analyzed the rare earth element concentrations in 100 small-volume samples from 9 cores in different parts of the Atlantis II Deep to better understand the origins of different types of metalliferous sediments (detrital, proximal hydrothermal and distal hydrothermal). Our results agree with earlier studies based on larger bulk samples that show the composition of the major depositional units is related to major changes in the location and intensity of hydrothermal activity and the amount of hydrothermal versus background sedimentation. In this paper, we address the origins of chemically distinct laminae (down to sub-millimeter) that correspond to ∼annual deposition. REE patterns clearly reflect 3 different sources (e.g., detrital, scavenging, direct hydrothermal input). Detrital REE that are delivered to the Deep from outside account for most of the REE in the sediments of the Atlantis II Deep, similar to BIF, and are unaffected by fractionation due to hydrothermal processes during deposition and diagenesis. Fe- and Mn-(oxy)hydroxides that form at the anoxic–oxic boundary scavenge REE from the brine pool as they settle. The Fe-(oxy)hydroxides contain a larger proportion of REE from seawater than any other sediment-type and also scavenge REE from pore waters after deposition. In contrast, the Mn-(oxy)hydroxides dissolve before deposition and thus function as transporting agents between seawater and the brine. However, there is little evidence for direct seawater influence in the REE geochemistry of the sediments (e.g., Y/Ho ratio). Non-ferrous sulfides form proximal to the hydrothermal vent source and inherit an hydrothermal REE pattern.The total REE content of the presently forming Fe-(oxy)hydroxides is very low due to limited input of REE into the brine. The largest proportion of non-detrital REE appears to have been deposited early in the history of the basin from an initial brine pool that was relatively enriched in REE, followed by a change in REE chemistry in later sediments. Similar abrupt changes in the REE chemistry of ancient chemical sediments may record similar processes, including changes in local basin evolution and input of REE from different sources.