Abstract This work, which was done within the Swedish nuclear waste management program, was carried out in order to increase the understanding of the mobility and fate of rare earth elements (REEs) in natural boreal waters in granitoidic terrain. Two areas were studied, Forsmark and Simpevarp, one of which will be selected as a site for spent nuclear fuel. The highest REE concentrations were found in the overburden groundwaters, in Simpevarp in particular (median ∑REE 52 μg/L), but also in Forsmark (median ∑REE 6.7 μg/L). The fractionation patterns in these waters were characterised by light REE (LREE) enrichment and negative Ce and Eu anomalies. In contrast, the surface waters had relatively low REE concentrations. They were characterised either by an increase in relative concentrations throughout the lanthanide series (Forsmark which has a carbonate-rich till) or flat patterns (Simpevarp with carbonate-poor till), and had negative Ce and Eu anomalies. In the bedrock groundwaters, the concentrations and fractionation patterns of REEs were entirely different from those in the overburden groundwaters. The median La concentrations were low (just above 0.1 μg/L in both areas), only in a few samples were the concentrations of several REEs (and in a couple of rare cases all REEs) above the detection limit, and there was an increase in the relative concentrations throughout the lanthanide series. In contrast to these large spatial variations, the temporal trends were characterised by small (or non existent) variations in REE-fractionation patterns but rather large variations in concentrations. The Visual MINTEQ speciation calculations predicted that all REEs in all waters were closely associated with dissolved organic matter, and not with carbonate. In the hydrochemical data for the overburden groundwater in particular, there was however a strong indication of association with inorganic colloids, which were not included in the speciation model. Overall the results showed that within a typical boreal granitoidic setting, overburden groundwaters are enriched in REEs, organic complexes are much more important than carbonate complexes, there is little evidence of significant mixing of REEs between different water types (surface, overburden, bedrock) and spatial variations are more extensive than temporal ones.