Scarce and unreliable urban water supply in many countries has caused municipal users to rely on transfers from rural wells via unregulated markets. Assessments of this pervasive water re-allocation institution and its impacts on aquifers, consumer equity and affordability are lacking. We present a rigorous coupled human–natural system analysis of rural-to-urban tanker water market supply and demand in Jordan, a quintessential example of a nation relying heavily on such markets, fed by predominantly illegal water abstractions. Employing a shadow-economic approach validated using multiple data types, we estimate that unregulated water sales exceed government licences 10.7-fold, equalling 27% of the groundwater abstracted above sustainable yields. These markets supply 15% of all drinking water at high prices, account for 52% of all urban water revenue and constrain the public supply system’s ability to recover costs. We project that household reliance on tanker water will grow 2.6-fold by 2050 under population growth and climate change. Our analysis suggests that improving the efficiency and equity of public water supply is needed to ensure water security while avoiding uncontrolled groundwater depletion by growing tanker markets.