The Gaza Strip coastal aquifer is affected by increasing salinity and falling groundwater levels. Several authors believe these processes are related to the increasing water demand in the Gaza Strip corresponding to population growth during the past few decades. According to this model, aquifer overexploitation will trigger seawater intrusion. In this paper, a new mechanism is proposed for water pollution, and guidelines for water management are presented. It has been suggested that there is a highly mineralized water inflow from the northern Negev area, through a preferential drainage axis. According to the new complete model, the following integrated guidelines for water management are drawn: (a) it is necessary to intercept the highly mineralized eastern groundwater along the Israel boundary; (b) water extracted has to be treated by desalination plants; (c) extraction of inflowing eastern water, characterized by good quality, would be prior to mixing between these mineralized and local infiltration waters; (d) the prevention of the mixing will allow production of a less mineralized groundwater in the Gaza Strip; (e) the total quality of waters utilized in Gaza Strip, in the framework of an integrated management programme, would increase if perched groundwater, demonstrated to occur in the dune sand bodies, were made available to local people.