This study investigates the characteristics and distribution of rare earth elements (REEs) within the multi-aquifer groundwater system of the Panxie mining area in the Huainan coalfield, China. By analyzing groundwater samples from various aquifers, including sandstone, limestone, and shale, the research provides a comprehensive assessment of REE content, fractionation patterns, and anomalies, with a particular focus on Ce and Eu. The results show that, except for the sandstone aquifer, the REE concentrations in other aquifers are generally lower than the global average for river waters, with notable Ce negative anomalies and Eu positive anomalies observed across the samples. Additionally, the study employs Visual MINTEQ software to model the inorganic complexation of REEs, revealing that carbonate complexes, such as Ln(CO₃)²⁻ and LnCO₃⁺, dominate in these groundwater systems. Finally, the research constructs a Fisher discriminant model for groundwater source identification, using the concentrations of 14 REEs as variables. The model demonstrates high accuracy, particularly in distinguishing between sandstone and limestone aquifers, offering valuable insights for groundwater management and protection in mining areas. The study not only enhances the understanding of REE geochemical behavior in groundwater but also provides a scientific basis for the development of more effective groundwater resource management strategies in the Panxie mining area and similar environments.