Deep groundwater is an important source of drinking water, and can be preferable to shallower groundwaters where they are polluted by surface-borne contaminants. Surface-borne contaminants are disproportionately common in ‘modern’ groundwaters that are made up of precipitation that fell since the ~1950s. Some local-scale studies have suggested that groundwater pumping can draw modern groundwater downward and potentially pollute deep aquifers, but the prevalence of such pumping-induced downwelling at continental scale is not known. Here we analyse thousands of US groundwater tritium measurements to show that modern groundwater tends to reach deeper depths in heavily pumped aquifer systems. These findings imply that groundwater pumping can draw mobile surface-borne pollutants to deeper depths than they would reach in the absence of pumping. We conclude that intensive groundwater pumping can draw recently recharged groundwater deeper into aquifer systems, potentially endangering deep groundwater quality.