Manganese enriched carbonates preferentially accumulate in near-shore, shallow water sediments of the Dead Sea. These carbonates are formed by coprecipitation of Mn with authigenic aragonite, as well as by direct precipitation of Mn-carbonate from the pore water of the shallow sediments. The primary source of the Mn that accumulates as carbonates is allochthonous Mn-enriched oxides that are eroded from the nearby coasts and become buried within the near-shore shallow water sediments. Due to the decline in the level of the Dead Sea between 1960–1990, bands of sediments (parallel to the current shoreline) which were previously submerged, became exposed to air and consequently desiccated. We suggest that in order to approach new hydraulic equilibrium in some of those coastal areas, the decline in the level of the lake was followed by a lakeward advance of fresher groundwater from the shallow coastal aquifer. Those fresher waters are characterized by a higher pH than the interstitial brine, and therefore a new state of water-rock interaction is established which results in oxidative alteration of Mn-carbonates to Mn-oxides. In addition, manganese-oxidizing bacteria, shown to be active in water with lower salinity than that of the Dead Sea, may also play a part in oxidation of divalent manganese released from the sediment. As a result, some segments of the Dead Sea coast are characterized by black Mn-enriched sediments that in places form crusts over the surface.