The Kalyus Beds of the late Ediacaran Nagoryany Formation occurring in the northeastern part of the Republic of Moldova are dominated by black argillites with phosphorites and calcareous concretions. Four lithological groups were examined with respect to their rare earth element (REE), major and trace element geochemistry: phosphorites, enriched argillites, pure argillites and carbonates. Phosphorites and enriched argillites exhibit a pronounced middle-REE bulge suggesting a strong diagenetic uptake of REEs. Y/Ho ratios are mostly <35, values that are consistent with derivation of >90% of REEs from lithogenous sources. Pure argillites show a flat REE distribution similar to that of average upper continental crust (UCC), indicating that REEs are likely related to detrital siliciclastics derived from felsic to mafic source rocks of the adjacent regions of Baltica, which was isolated within paleo-oceans during the late Ediacaran. Carbonates show a light-REE depleted pattern with relatively high Y/Ho ratios (up to 53) that suggests the preservation of a predominantly hydrogenous (seawater-derived) REE signal. Ce/Ce* ratios of ∼0.80–1.02 reflect suboxic to anoxic seawater conditions. This is a locally and temporally constrained anoxic event, since widespread oxic conditions were specific for the continental margins of Baltica. The phosphorites and enriched argillites groups of the Kalyus Beds show high middle-REE enrichment comparable to those of other known world phosphorite deposits. Their total REE contents are high (793–1735 ppm) and are of potential economic interest. These results provide insights for expanding global REE exploration targets and may have implications for a better understanding of the depositional environments during the late Ediacaran.