The large volume of deep groundwater in the Precambrian crust has only recently been understood to be relatively hydrogeologically isolated from the rest of the hydrologic cycle. Currently, the paucity of permeability measurements in the Precambrian crust is a barrier to modeling fluid flow and solute transport in these low porosity and permeability deep environments. Estimates of permeability from prograde metamorphic rocks and geothermal systems have been applied to such groundwater systems, but, as data are few, it is unclear how appropriate this is for Precambrian crust on a global scale. To resolve this, we apply a new approach to constrain permeabilities for Precambrian crust to depths of 3.3 km based on fluid residence times estimated from noble gas analyses. The additional data reveals there is no statistically significant relationship at depths below 1 km, challenging the previous assumption of a global correlation between permeability and depth. Additionally, we show that estimated permeabilities at depths >1 km are at least an order of magnitude lower than previous estimates and possibly much lower. As a consequence, water and solute fluxes at these depths will be extremely limited, imposing important controls on elemental cycling and the distribution of subsurface microbial life.