The Paleoproterozoic Seligdar magnesiocarbonatite intrusion of the Aldan-Stanovoy shield in Russia underwent extensive postmagmatic hydrothermal alteration and metamorphic events. This study comprises new isotopic (Sr, Nd, C and O) data, whole-rock major and trace element compositions and trace element characteristics of the major minerals to gain a better understanding of the source and the formation process of the carbonatites. The Seligdar carbonatites have high concentrations of P2O5 (up to 18 wt%) and low concentrations of Na, K, Sr and Ba. The chondrite-normalized REE patterns of these carbonatites display significant enrichments of LREE relative to HREE with an average La/Ybcn ratio of 95. Hydrothermal and metamorphic overprints changed the trace element characteristics of the carbonatites and their minerals. These alteration processes were responsible for Sr loss and the shifting of the Sr isotopic compositions towards more radiogenic values. The altered carbonatites are further characterized by distinct 18O- and 13C-enrichments compared to the primary igneous carbonatites. The alteration most likely resulted from both the percolation of crustal-derived hydrothermal fluids and subsequent metamorphic processes accompanied by interaction with limestone-derived CO2. The narrow range of negative εNd(T) values indicates that the Seligdar carbonatites are dominated by a homogenous enriched mantle source component that was separated from the depleted mantle during the Archean.