Measurements of gas compositions and emission rates play a major role in monitoring restless volcanoes. However, thermodynamic calculations imply that scrubbing by groundwater will prevent most HCl and significant SO2 emissions until dry pathways are established, thus leading to underestimates of gas released from magma and magma volumes. Despite the significance, direct evidence for scrubbing is mostly lacking. Based on 50 water samples collected between 2003 and 2011 from the deep NSF Well at the summit of Kīlauea Volcano we show that the chemical and stable isotope compositions of groundwater were modified by magmatic gas condensation. Temporal variations of dissolved SO42- and Cl- in the water coincided with changes in magmatic and volcanic activity. In 2006 up to ~40% of the SO2 and HCl degassed from magma may have been scrubbed by groundwater.