Groundwater is the principal source of public water supply and for satisfying the daily water needs. The Gaza strip coastal aquifer is suffering from salinity and contamination due to human activities especially agriculture activities. Although, the nitrate is necessary for agriculture activities it can affect the groundwater quality if leached nitrate from the soil into freshwaters after some time. The main objective of this research is to evaluate the current situation of the Gaza strip coastal aquifer and to predict the nitrate concentrations resulting from agriculture activities over the next twenty years using modelling approach. 3D Numerical groundwater flow modeling was developed to simulate the impacts of transport of nitrate loading from agricultural land on groundwater system using finite difference method GMS 10.4 software (MODFLOW 2005 code and MT3DMS package). Five management scenarios were considered to study the effect of pumping and recharge parameters on the groundwater flow system and the impacts of transport of nitrate loading from agricultural areas on the aquifer. Ten different wells were selected to investigate the impact of management scenarios on the nitrate concentration. All management scenarios indicated that there is a relationship between the water level and nitrate concentration in aquifer therefore the rates of nitrate concentration in the southern regions of Gaza strip is more than the northern regions.