Water samples from different aquifers in Gboko area, Lower Benue Trough, Nigeria, were evaluated to determine the quality, hydrochemical facies and the concentrations and fractionation patterns of rare earth elements (REEs) in the groundwater. The results revealed that the groundwater is contaminated with factors emanating from the concentrations of NO3, Cl, Mn, and the TDS (total dissolved solids). Five hydrochemical facies were identified, namely Na + KSO4Cl, Na + KHCO3, MgSO4Cl, and two forms of CaMgHCO3 (viz., Na + KHCO3 and Na + KSO4Cl). Ion exchange leads to the formation of Na + KHCO3 from CaMgHCO3, while reversed ion exchange leads to the formation of Na + KSO4Cl from CaMgHCO3, usually in the presence of saline water conditions. Also, simple dissolution or linear mixing gives rise to CaMgSO4Cl from CaMgHCO3. The results also showed that the contents of REE in the samples range from 1 to 445 ppb, with significant contributions from La, Ce and Nd. The shallow groundwater is predominantly LREE-enriched NASC-normalized patterns. The LREE enrichment is attributed to weathering of host rock minerals, such as phosphate monazite, florencite, and allanite, in an oxic environment, while the HREE enrichment is attributed to processes such as complexation reactions, desorption processes, re-adsorption processes, and chemical weathering in a reducing condition. The groundwater shows positive anomalies for both Ce and Eu. The Ce is controlled by oxidation of Ce3+ to Ce4+, incorporation of Ce into Mn and Fe oxyhydroxides phases, and Eu anomalies by weathering of zircon-rich minerals.