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This study aimed to investigate the REEs' presence in the rocks and groundwaters of three different aquifers in eastern Crete. The first develops in carbonate rocks, and is a typical unconfined karst aquifer. The second, develops in Miocene conglomerates and sandstones, and is confined by marly formations, while the third in the Pliocene conglomerates overlying the Phyllites Formation. They are all formed by minerals such as calcite, dolomite, aragonite, anhydride, halite and sylvite, display neutral to slightly alkaline pH and positive to slightly positive redox values. The karst aquifer is of Ca-Mg-HCO3 water type, while near the coast Na+ and Cl− are also involved due to seawater intrusion. In the other two aquifers, complex hydrochemical types prevail such as, Ca-Mg-Na-HCO3-Cl for the second or Na-Ca-Mg-Cl-HCO3 for the third one. ΣREEs concentrations range between 64 and 1,671 ppm for rocks, 45 and 120 ppt for 0.45 μm filtered, and 219 and 1,087 ppt for unfiltered groundwater. The differences between filtered and unfiltered samples were attributed to the greater tendency of REEs to be adsorbed on surfaces such as Fe-Mn oxides and hydroxides, some organic substances or particles, colloids, clay minerals, and microorganisms, which were removed during filtration. Furthermore, an evident negative Ce anomaly in the filtered samples was attributed to the Ce oxidation and removal from the dissolved phase. The Japanese and European shales normalised REE diagrams of all groundwater samples show great similarities attributed to the presence of common major minerals such as calcite, dolomite and gypsum. The positive Eu anomalies were attributed to the dissolution of these common minerals from the aquifers' bedrock. Finally, the increased concentrations in the unfiltered samples of the porous aquifers were associated with ion exchange processes, while the lower values in certain brackish samples were attributed to colloidal precipitation processes due to the increased salinity. [ABSTRACT FROM AUTHOR]