Abstract Groundwater recharge feeds aquifers supplying fresh water to a population over 80 million in Iran – a global hotspot for groundwater depletion. Using a rich database comprising abstractions from about 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 primarily caused by unsustainable development. Our results show the annual average 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 national surface water resources are seeping into the groundwater basins. Such decline in groundwater recharge could further exacerbate the already dire groundwater depletion situation in Iran with devastating consequences for the country’s natural environment and socio-economic development, locally increasing food prices, and limit exports of agricultural products to neighboring countries that are major oil and gas producers in the world.