In Cisjordan, surface- and groundwater flow are either towards the Jordan Valley–Dead Sea–Arava Valley (the Rift) or the Mediterranean Sea. Due to upstream exploitation by riparians to the Jordan River, the historical annual flow, which fluctuated between 250 and 1100 Mm 3, has declined to a mere 100–200 Mm 3. The remaining flow south of Lake Kinneret is highly polluted and heavily loaded with salts. Lake Kinneret (Sea of Galilee) is one of the major water resources in the area. Annually, between 200 and 700 Mm 3 reach the Lake as surface and groundwater flow. The relatively high salinity of the Lake is caused by thermomineral water discharging from springs and seepages located onshore and on the bottom of the Lake. The main factors causing deterioration of the groundwater quality in the Rift are of geogenic character. These are different types of brines, whose outflow and penetration into freshwater aquifers was triggered by overpumpage. Contemporary encroachment of seawater caused by intensive water exploitation in the Coastal Plain is manageable and reversible. However, due to lack of hydrogeological evidence, no such statement can be made about the circulation of seawater beneath the Coastal Plain and into the deep-seated Yarkon–Taninim aquifer or the upflow of brines in the Rift. The flow regimes of the different brine bodies could not be elucidated. Whether each such brine-body flows by its particular hydrological regime or whether the movement of the different bodies is intradependent or interdependent with the regional movement of fresh groundwater, remain open questions. Therefore, sustainable development of groundwater resources is clearly dependent on the elucidation of the relationship between changes in the pressure of the brine with depth and its relationship to the overlying freshwater. The average total annual recharge of all water sources in Cisjordan is 1820 Mm 3, which means that the total production of water must be managed within the limits of this annual volume. During drought years, total groundwater extraction exceeds the safe yield, causing drastic lowering of water levels and upflow of saline waters from greater depths. Because of the structural complexity of aquifers and hydrochemical variability of the numerous groundwater bodies, new hydrochemical methods have been developed for the identification of groundwater bodies and for the elucidation of their origins. These methods combine macrochemical, microchemical, and isotopic evidences. By combining distribution patterns of rare earths, yttrium and stable isotopes, a complete picture of catchment lithology and the altitude and latitude of precipitation could be obtained. The area west of the Jordan River is characterized by the occurrence of transboundary surface- and groundwater basins in which fresh and saline water and brines flow across political borders between Israel and the Palestinian Authority. It is very difficult to assess separately the annual safe yield of water resources for each of the two national entities. Neither country may dispose independently of its waters and is usually at the mercy of the other riparian. There is as yet no general multilateral international treaty in force allocating the water resources of international watercourses. At present there are two rules for the management of the waters of an international drainage basin—the rule of Equitable Distribution, and the obligation Not to Cause Significant Harm. The rules of equitable distribution have tended to focus on the issue of quantities of water rather than on quality of water, which is really relevant to the issue of equitable distribution. Future negotiations on the uses of the basin will need to deal with issues of characteristic salinities and geochemical features and on their impact on equitable sharing of water resources.