Groundwater in the northeastern Amman-Zarqa basin is an important source of water for irrigation. The quality and quantity of water has deteriorated due to mismanagement and misunderstanding of the hydrogeological system. Overexploitation of groundwater resources upstream of the Khirbet Al-Samra wastewater treatment plant (KSWTP) has lowered the water table 43 m since the beginning of groundwater development in 1968. Heavy pumping of groundwater downstream of KSWTP has not dropped the water level due to constant recharge from the Zarqa river bed. The water level of groundwater is rising continuously at a rate of 20 cm per year since building the KSWTP in 1985. Groundwater salinity has also shifted the quality of the aquifer from fresh to brackish. Continual irrigation from the groundwater upstream of KSWTP dissolves accumulated salt from the soil formed by evaporation, and the contaminated water infiltrates back to the aquifer, thereby increasing both salt and nitrate concentrations. The intense irrigation from the reclaimed water downstream of KSWTP and leakage of treated wastewater from the Zarqa River to the shallow groundwater is a secondary source of salt and nitrates. The isotopic composition of groundwater varies over a wide range and is associated with the meteoric water line affected by Mediterranean Sea air moisture. The isotopic composition of groundwater is represented by evaporation line (EL) with a low slope of 3.6. The enrichment of groundwater in d18 O and dD is attributed mainly to the two processes of evaporation before infiltration of return flow and mixing of different types of water in KSWTP originating from different aquifers. The EL starts from a location more depleted than the weighted mean value of the Amman rainfall station on the Eastern Meteoric Water Line indicating that the recharge took place under the climate regime prevailing today in Jordan and the recharge of the groundwater originates from a greater elevation than that of the Amman station. Elevated high tritium levels observed in wells in close proximity to a regional fault system signify local recharge and short residence time. The Khaldyia dam is a local source for groundwater recharge.