Potential environmental issues associated with the mining of carbonatites are receiving increased attention due to the importance of critical metals for green technologies. This study investigates the chemistry of tailings seepage at the former Saint Lawrence Columbium mine near Oka, Québec, Canada, which produced pyrochlore concentrate and ferroniobium from a carbonatite-hosted Nb-REE deposit. Detailed field sampling and laboratory methods were used to characterize the hydraulic properties of the tailings, their bulk chemistry, mineralogy, pore water and effluent chemistries. The tailings are composed of REE-enriched calcite (64–89 wt %) and fluorapatite (2–22 wt %), as well as biotite (6–17 wt %) and chlorite (0–7 wt %). Minor minerals include ankerite, pyrite, sphalerite, molybdenite, magnetite and unrecovered pyrochlore. Secondary minerals include gypsum, barite, strontianite and rhodochrosite. Geochemical mass balance modeling, constrained by speciation modeling, was used to identify dissolution, precipitation and exchange reactions controlling the chemical evolution of pore water along its flow path through the tailings impoundment. In the unsaturated zone, these reactions include sulfide oxidation and calcite dissolution with acid neutralization. Below the water table, gypsum dissolution is followed by sulfate reduction and FeS precipitation driven by the oxidation of organic carbon in the tailings. Incongruent dissolution of biotite and chlorite releases K, Mg, Fe, Mn, Ba and F and forms kaolinite and Ca-smectite. Cation exchange reactions further remove Ca from solution, increasing concentrations of Na and K. Fluoride concentrations reach 23 mg/L and 8 mg/L in tailings pore water and effluent, respectively. These values exceed Canadian guidelines for the protection of aquatic life. In the mildly alkaline (pH 8.3) pore waters, Mo is highly mobile and reaches an average concentration of 83 μg/L in tailings effluent, which slightly exceeds environmental guidelines. Concentrations (unfiltered) of Zn reach 1702 μg/L in tailings pore water although values in effluent are usually less than 20 μg/L. At the ambient pH, Zn is strongly adsorbed by Fe–Mn oxyhydroxides. Although U forms mobile complexes in tailings pore water, concentrations do not exceed 16 μg/L due to the low solubility of its pyrochlore host. Adsorption and the low solubility of pyrochlore limit concentrations of Nb to less than 49 μg/L. Cerium, from calcite dissolution, is strongly adsorbed although it reaches concentrations (unfiltered) in excess of 1 mg/L and 100 μg/L in pore water and effluent, respectively. Results of this study show that mine tailings from carbonatite deposits are enriched in a wide variety of incompatible elements with multiple mineral hosts of varying solubility. Some of these elements, such as F and Mo, may represent contaminants of concern because of their mobility in alkaline tailings waters.