A systematic measurement of ions and 2H/1H, 7Li/6Li, 11B/10B, 18O/16O, and 87Sr/86Sr isotopes in feed-waters, permeates, and brines from commercial reverse osmosis (RO) desalination plants in Israel (Ashkelon, Eilat, and Nitzana) and Cyprus (Larnaca) reveals distinctive geochemical and isotopic fingerprints of fresh water generated from desalination of seawater (SWRO) and brackish water (BWRO). The degree of isotope fractionation during the passage of water and solutes through the RO membranes depends on the medium (solvent-water vs. solutes), chemical speciation of the solutes, their charge, and their mass difference. O, H, and Sr isotopes are not fractionated during the RO process. 7Li is preferentially rejected in low pH RO, and B isotope fractionation depends on the pH conditions. Under low pH conditions, B isotopes are not significantly fractionated, whereas at high pH, RO permeates are enriched by 20‰ in 11B due to selective rejection of borate ion and preferential permeation of 11B-enriched boric acid through the membrane. The specific geochemical and isotopic fingerprints of SWRO provide a unique tool for tracing "man-made" fresh water as an emerging recharge component of natural water resources.