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The Pleistocene aquifers are important sources of water supply in both the Gaza and Jericho areas of Palestine. The aquifers are saline with freshwater lenses floating on saline bodies of water. It is important to investigate how to exploit these freshwater lenses without causing unnecessary mixing of the fresh and saline waters. The objective of this research is to investigate the feasibility of applying skimming and scavenger pumping as a means to exploit the freshwater lenses and to control saline water upconing in the aquifers. This study is the first to examine the movement of fresh and saline waters underneath skimming and scavenger wells in the aquifers of Gaza and Jericho. Two simulation models that couple density-dependent fluid flow and solute transport have been used to simulate and predict the movement of saltwater under different hydrogeological and operational conditions of skimming and scavenger wells in the two aquifers. The results show (for the Jericho Aquifer) that: the location of well screen has a strong control on the steady-state position of the fresh/saline water transition zone; the upconing mechanism appears to continue under skimming pumping until saline water enters the well screen even when the pumping rate is reduced; and for better salinity control it is necessary to place well screen against the gravel layers only and locate one screen segment in the saline water zone. The study shows (for the Gaza coastal aquifer) that the most important parameters affecting the movement of saline water under scavenger pumping are the relationship between recharge and pumping rates, the location of the well screen within the saturated thickness, the vertical permeability; and the transverse dispersivity. This study shows that saltwater upconing in Gaza aquifer can be controlled by operating a second well in the saline water zone so that the optimal ratio between saline water and freshwater pumping is 1:2 respectively.