Rare earth elements (REEs) combined with yttrium (YREE) in deep groundwater from granite and fracture-filling calcite are being studied at the Mizunami Underground Research Laboratory (MIU, Tono area, central Japan). The groundwater was sampled from cored boreholes drilled from the MIU galleries at 200, 300, 400 and 500m depths. The fracture-filling calcite was collected from the same boreholes and dissolved in 1M NH4 acetate buffer solution (pH4.8). Major chemical composition of groundwater changed with depth; and the concentrations of some major elements (Na+, K+, Ca2+ Mg2+, Cl−, Br− and B) increased with depth, while alkalinity, SO42−, and F− decreased. Isotopic compositions of δ18O and δD indicated that the groundwater originated from meteoric water. YREE patterns of groundwater also changed with depth; with heavy REE (HREE) enrichment in “shallow” groundwater (−200 to −400m) and light REE (LREE) enrichment in “deep” groundwater (−500m). The predominant YREE species are YREECO3+ and YREE(CO3)2− (LaCO3+: 65–70%, La(CO3)2−: 8–27%, LuCO3+: 20–38% and Lu(CO3)2−: 53–77%). The LREE enrichment in the “shallow” groundwater resulted in preferential scavenging of positively charged YREECO3+ by negatively charged bedrock surfaces in slightly alkaline groundwater pH (7.4–8.6). Because of the construction and operation of the underground facility, the “shallow” groundwater has been influenced by infiltration of surface water undersaturated in calcite. In contrast, the “deep” groundwater was barely affected by the mixing of surface water, indicating that the YREE originated from YREE fractionation by bedrock granite. Irrespective of depth, a negative Ce anomaly preserved in the groundwater, is probably indicative of paleo-oxic conditions during paleo-recharge. The negative Ce anomaly in the groundwater was possibly fractionated from sedimentary calcite with positive Ce anomalies during the paleo-recharge. The YREE patterns of the fracture-filling calcite were enriched in LREE. The isotopic variations of δ18O and δ13C in the fracture-filling calcite indicated that it originated from a mixture of sea water and fresh water at a temperature <100°C. The YREE patterns of paleo-groundwater from which the fracture calcite precipitated were calculated using YREE abundances in the fracture calcite and distribution coefficient reported in previous laboratory experiments. The paleo-groundwater was found to be enriched in LREE and HREE depending on the aqueous YREE species. Our results suggest that changes in the paleo- to present-day YREE fractionation range roughly from that of present-day shallow to deep groundwater.