Water scarcity has led to wide use of reclaimed water for irrigation worldwide, which may threaten groundwater quality. To understand the status of groundwater in the reclaimed water irrigation area in Beijing, 87 samples from both shallow and deep aquifers were collected to determine the factors affecting groundwater chemistry and to assess groundwater quality for drinking and irrigation purposes. The results show that groundwater in both shallow and deep aquifers in the study area is weakly alkaline freshwater with hydrogeochemical faces dominated by HCO3-Na·Mg·Ca, HCO3-Mg·Ca·Na, HCO3-Ca·Na, and HCO3-Na. The chemical composition of groundwater in both shallow and deep aquifers is dominantly controlled by the dissolution of halite, gypsum, anhydrite, and silicates weathering, as well as ion exchange. Geogenic processes (rock weathering and ion exchange) are the only mechanisms controlling groundwater chemistry in deep aquifers. Besides geogenic processes, evaporation and anthropogenic activities also affect the chemistry of shallow groundwater. Quality assessment reveals that both shallow and deep groundwater are generally suitable for drinking and irrigation purposes. The quality of deep groundwater is more excellent for drinking than shallow groundwater. However, long-term use of deep groundwater for irrigation exhibits higher potential risks to deteriorate soil property due to the relative higher permeability indexes (PI). Therefore, it is recommended that deep groundwater is preferentially used for drinking and domestic purpose, and shallow groundwater for agricultural irrigation.