Most rivers exchange water with surrounding aquifers. Where groundwater levels lie below nearby streams, streamwater can infiltrate through the streambed, reducing streamflow and recharging the aquifer. These ‘losing’ streams have important implications for water availability, riparian ecosystems and environmental flows, but the prevalence of losing streams remains poorly constrained by continent-wide in situ observations. Here we analyse water levels in 4.2 million wells across the contiguous USA and show that nearly two-thirds (64 per cent) of them lie below nearby stream surfaces, implying that these streamwaters will seep into the subsurface if it is sufficiently permeable. A lack of adequate permeability data prevents us from quantifying the magnitudes of these subsurface flows, but our analysis nonetheless demonstrates widespread potential for streamwater losses into underlying aquifers. These potentially losing rivers are more common in drier climates, flatter landscapes and regions with extensive groundwater pumping. Our results thus imply that climatic factors, geological conditions and historic groundwater pumping jointly contribute to the widespread risk of streams losing flow into surrounding aquifers instead of gaining flow from them. Recent modelling studies have suggested that losing streams could become common in future decades, but our direct observations show that many rivers across the USA are already potentially losing flow, highlighting the importance of coordinating groundwater and surface water policy.