Groundwater recharge feeds aquifers supplying fresh-water to a population over 80 million in Iran—a global hotspot for groundwater depletion. Using an extended database comprising abstractions from over one million groundwater wells, springs, and qanats, from 2002 to 2017, here we show a significant decline of around −3.8 mm/yr in the nationwide groundwater recharge. This decline is primarily attributed to unsustainable water and environmental resources management, exacerbated by decadal changes in climatic conditions. However, it is important to note that the former’s contribution outweighs the latter. Our results show the average annual amount of nationwide groundwater recharge (i.e., ~40 mm/yr) is more than the reported average annual runoff in Iran (i.e., ~32 mm/yr), suggesting the surface water is the main contributor to groundwater recharge. Such a decline in groundwater recharge could further exacerbate the already dire aquifer depletion situation in Iran, with devastating consequences for the country’s natural environment and socio-economic development.