The lower sub-aquifers of the Mediterranean coastal aquifer of Israel, at the Palmahim area, are hypothesized to be laterally blocked to connection with the sea, and thus to seawater intrusion. This is mostly due to the detection of fresh water bodies at these sub-aquifers. This study examine this hypothesis by using two dimensional numerical model simulations of the groundwater flow system at this area, which conducted in order to reveal which hydrogeological setting enables the existence of these fresh water bodies in the lower sub-aquifers and to assess the on-land pumping rates that will prevent their salinization. The hydrogeological settings were examined by steady state simulations followed by simulations of the last 15,000 years sea level changes. These simulations imply that the presence of fresh water in the lower sub-aquifer, whether blocked or connected to the sea, requires offshore separation between the upper and lower sub-aquifers. On-land pumping simulations, with a well located inside the lower sub-aquifers at the shoreline, show a maximum pumping rate of 250 m 3 /m strip width/year, hereafter m 2 /year, to prevent the salinization of the lower subaquifers. The various pumping scenarios revealed differences in salinization trends between the scenarios with impermeable separating layers and those with semi permeable layers. Scenarios with extreme pumping rates emphasize these differences, and together with field test, can allow assessing the amount of separation between the sub-aquifers.