Rainwater was sampled during seven winters at eight sites along the Jordan Rift valley in Israel. The study area is divided into two regions: the northern part located between the Sea of Galilee and the Dead Sea and the southern part between the Dead Sea and the Dead Sea-Red Sea water divide line in the Arava valley. The Dead Sea region is considered as a desert, the northern part of the study area is semidesert whereas the southern region is considered as extreme desert. Good agreement was found between the chemical and isotopic composition of rainwater its sources and air mass trajectories. In the arid areas, the contribution of salts was mainly from local sources (of up to 500 Km in diameter). Significant chemical divergence was found between rainwater deriving from marine air masses characterized by NaCl enrichment and rainwater deriving from continental air masses which are mainly characterized by Ca-carbonate enrichment. Six main marine and continental air mass trajectories were defined, i.e., northern, northwestern, western, southwestern, eastern and local. The northern air mass trajectories contribute more salts than the southwestern air mass trajectories which, exhibit the lowest rainwater salinities. The western trajectory is exclusively marine originating from the Mediterranean, while the eastern trajectory is exclusively continental and originates in the Arabian Desert. Rainwater isotopes revealed three chemically differing systems. The western marine trajectories reflect chemical setting associated with East Mediterranean Meteoric Water Line system; the continental air masses are mainly associated with the Mean Meteoric Water Line system; and whenever the eastern component is significant, a Local Meteoric Water Line prevails.