Although carbonatites are the primary source of the world’s rare earth elements (REEs), the processes responsible for ore-grade REE enrichment in carbonatites are still poorly understood. In this study, we present a petrologic, geochemical, and isotopic evaluation of the Elk Creek carbonatite in southeast Nebraska to constrain the origin of REE mineralization. The Elk Creek carbonatite is a multilithologic carbonatite comprised of an early apatite-dolomite carbonatite, a middle/heavy REE-enriched magnetite-dolomite carbonatite, and a late-stage light REE-enriched, barite-dolomite carbonatite, as well as a suite of breccias. Neodymium, strontium, and carbon isotopic data from the early apatite-dolomite carbonatite, ε_Nd(T) = 2.3 to 3.4, ⁸⁷Sr/⁸⁶Sr_(i) = 0.702704 to 0.702857, and δ¹³C = −3.3 to −3.4, indicate that the parental magma and REEs were derived from the mantle, and textural and chemical data suggest that hydrothermal processes played an important role in reaching ore-grade enrichment. Higher initial ⁸⁷Sr/⁸⁶Sr values (∼0.7041) of REE-mineralized lithologies are evidence that these fluids were derived, in part, from meteoric water that interacted with the country rock. Modeling of the C-O isotopic data reveals that some of the isotopic variation results from closed-system Rayleigh fractionation of an evolving carbonatitic magma between 300 and 500 °C, but an excursion to heavier δ¹⁸O is likely the result of interaction with H₂O-CO₂-fluids at temperatures from 400 to 100 °C. Hydrothermal dolomite has higher ⁸⁷Sr/⁸⁶Sr values than early-formed magmatic dolomite, consistent with metasomatism by fluids derived, in part, from a more radiogenic source such as the Precambrian-age wall rock. Rare earth element mineralization occurs primarily in fine-grained, cavity filling minerals including monazite, bastnäsite, parisite, and synchysite along with barite, dolomite, quartz, and iron oxides. We interpret the LREE enrichment at Elk Creek to be the product of hydrothermal fluids derived from the evolving carbonatite magma and fluids from the wall rock. The REEs likely became enriched in late-stage fluids from the evolving magma as well as being remobilization by the dissolution of earlier formed minerals. Middle/heavy REE-enrichment in the magnetite-dolomite carbonatite is hosted in hydrothermal dolomite and is attributed to variations in the composition of hydrothermal fluids.