Rare earth elements and Y (REY) have been analysed in 49 groundwaters from localities in the areas of Lake Kinneret and the Jordan and Arava Valleys. These waters originate from various aquifers and the REY abundances are expected to be controlled by the aquifer rocks. The REY pattern allow one to distinguish interaction of waters with basalts, basalt-limestone interaction zones (silicified limestones), limestones from the Judea and Avdat Groups (Upper Cretaceous and Eocene, respectively), and sandstones of the Lower Cretaceous Kurnub Group. Groundwater from the Quaternary alluvial fill (Dead Sea Group) are either controlled by Judea Group limestone or Kurnub Group sandstone. The REY patterns show characteristic features for each group. In hydrogeological systems, the rocks of natural replenishment areas are usually not the same as rock units from which the waters are collected. This becomes evident by comparing the lithostratigraphic groups from which the waters were collected and the hydrochemical grouping according to REY patterns with their characteristic trends and anomalies. In many cases, there is a correspondence between the lithostratigraphic and the hydrochemical grouping; in other cases, the 2 groupings disagree. This disagreement proves inter-aquifer flow of groundwater. In some cases, the geologically derived aquifers rocks of origin, differ from those indicated by REY patterns. Thus, applying the REY grouping, new fundamental information for hydrological models can be given and sources of salinisation can be elucidated.