This study was carried out at the Southern part of the coastal aquifer in the Gaza Strip (KhanYounis and Rafah Governorates) considering its geological and hydrogeological characteristics, water quality and water balance. This study is an attempt to find out the natural and anthropogenic reasons impact on the deterioration of groundwater in this part. All needed data are collected from many of relevant Palestinian Ministries. For determination status of groundwater quantity and salinity (suitability) for domestic use, Cl concentration in the pumped water and water level maps have been drawn with their relationship with distribution of abstraction rates. Rainfall distribution maps and aquifer lithological cross sections have been drawn also to determine their roles on the groundwater situation. The collected data are shows that; the total population rate has been increased during period 2000 to year 2010 with about 37.14% followed by rising water demand of both sectors domestic and agricultural in the study area. Study area is affected by climate change, where annual rainfall has a significant spatial and temporal variation; therefore, there are unpredicted fluctuations in number of rainy days accompanied by volatility and an unexpected drop in the amount of precipitation in this area. Infiltrated rainwater to the groundwater was affected by rainfall quantity decline. The average recharge water quantities don't adequate to cover water needs for irrigation purpose in this area. The average water quantities for irrigation purposes in the period (2000-2010) is 38.5Mm3/yr. Regarding to domestic water use, number of municipal wells gradually increased from 25 wells in 2000 to 67 wells in 2010, 43% of them have high pumping rates arrived to 180 m3/hr higher than of the average rate that recommended by PWA (70m3/hr). Extracted quantity of groundwater for domestic use in 2000 is 14Mm3, this quantity increased by 54.8% in 2010 to reach 22.3Mm3. The result shows that costal aquifer is dynamic system subjected to continuous change of an inflows and outflows, where net water outflow exceed water inflow. Hence, net aquifer balance is negative. It found also, that the impact of water deficit evident in lowering water table during the study period is about 8m, this decline matching with presence of municipality wells that have high production rates. Cone of depression has declined more and more every year with drilling new wells, as well as to spread huge number of agricultural wells in the same depletion area. Hence, this deterioration reflects an increase of Cl concentration in the areas that suffer from low water level. Cl concentration value is varied in the drinking wells depends on depth and locations of these wells. Percentage of suitable wells that have Cl concentration matching with WHO standards (<250mg\l) is 27% from total wells that distributed in the study area. Subsurface lithological structure has been drawn to determine the natural reasons behind the groundwater deterioration. Cross sections had shown the shortage of storage capacity of high quantities of fresh water in the coastal aquifer in the study area. Those sections show presence of clay that reduces the replenishment processes for the aquifer from the rainfall and returns flow from agricultural activities. So, lithological formation was evident as one of the natural causes which accelerate destroying process of the coastal aquifer, particularly with presence different clear in lithological structure within different places of the Gaza Strip comparing in the study area, which in turn provides the opportunity to the aquifer for increasing the storage capacity, as it clear in the North of Gaza Strip. Severe deterioration of the quality and quantity in the groundwater resources had been happened in this part of the Gaza Strip as a result of overexploitation of the groundwater and unsound environmental management conditions. So, quick decisions must be taken to reduce at least this crisis and to begin in providing well management for this only and very important resource.