To investigate the geochemistry of rare earth elements in groundwater from the Taiyuan Formation limestone aquifer, the concentrations of rare earth elements (REEs) were determined by ICP-MS for groundwater and limestone samples collected from the Taiyuan Formation limestone aquifer in the Wolonghu Coal Mine, Anhui province, China. The results shown that the groundwater is characterized by warm temperature (ranging from 35.8 to 39.1 °C), circum-neutral pH (7.34–8.27) and high total dissolved solids (TDS, 1380– 2850 mg/L). The REEs in groundwater are characterized by light rare earth elements (LREEs) depletion relative to heavy rare earth elements (HREEs), positive Eu anomalies and negative Ce anomalies. The fractionation of REEs in groundwater can be effected by the inorganic species of REEs. The negative Ce anomalies probably reflect the signature of the aquifer rocks (limestone rocks), whereas positive Eu anomalies are probably attributed to the redox conditions. The similarities of REE patterns between groundwater and aquifer rocks suggest that aquifer rocks play important roles in controlling the REE characteristics of groundwater. The characteristics of REEs and major ions in groundwater from the Taiyuan Formation aquifer are different from other aquifers in the Wolonghu Coal Mine.