Qatar is a hyper-arid country in the northeastern coast of the Arabian Peninsula. Over the last five decades, the built environment in the country’s metropolitan Doha, the capital city in Qatar, grew 60 times. Future plans include extra-urban development before 2030. Tough, the impact of such urban development on the country’s aquifers still unexplored. This study quantifies such impact through the end of the century. First, six periods represented the main stages of urban development during the last five decades in Doha. These periods are 1987, 1991, 1998, 2003, 2009, and 2013. Then, climatic data and groundwater parameters in addition to land use maps were used in a physically-based spatially distributed hydrological model (WetSpass) to calculate groundwater recharge values during these six periods. The variations in groundwater recharge quantities were then quantified spatially and temporally. Results showed significant variations with a deficiency in groundwater recharge increases with urban development increase. Groundwater recharge value in 2013 was 62% lower than that in 1987. Results also showed a particular trend of spatial variations in groundwater recharge. The study finally determined the main spots for applying managed aquifer recharge (MAR) as ways to replenish the aquifers. The findings of this study are keys to understanding the consequences of urban development changes in groundwater recharge, including impacts on agriculture and water balance. The proposed approach is applicable in similar regions, characterized by hasty urban development.