Rubidium and lithium are rather rare elements in environmental research, despite their affiliation with a group of chemically active metals and the abundance of Rb in the environment. A growing body of evidence, although controversial, has indicated that both elements possess unique essential and neurophysiological characteristics in biota and humans. Both elements may concentrate in soil and vegetation of sub-arid environments. We investigated the content and (potential) availability of Rb and Li in the soils and natural waters of Galilee, the Coastal Plain, and the northern Negev of Israel. A newly developed chromatographic technique for the separation of truly dissolved Rb and Li compounds has been applied. High concentrations of Rb, together with high values of the potentially vital Rb-to-K ratio, were found in the soils, the soil solutions, rainwater, throughfall water, and the plant litter leachates, but not in the surface and spring waters. This may indicate a sequestration of Rb in the local soils and a semi-closed Rb turnover in the soil-plant system with a major input from sea aerosols. Low Li bulk and available concentrations were determined in all the natural compartments. Possible implications of such specific environmental features on the local population health were discussed.