Hypocenter estimation at active volcanoes improves our understanding of their magmatic systems and indicates changing conditions at depth for continuously monitored volcanoes. The most active volcano in the Cascades Range, Mount St. Helens, has a multi-decadal earthquake catalog and it shows an apparent change in the depth distribution of seismicity before and after the 2004–2008 dome-building eruption and unrest sequence. We use two new resources to evaluate the accuracy of hypocenters and consequently the change in depth distribution of seismicity before and after the 2004–2008 eruption. First, we deployed a dense array of 136 three-component nodal seismographs for one month in 2017, including sub-arrays on the newly extruded dome and crater floor. Second, for events recorded during this month, we located their hypocenters using a three-dimensional (3D) wavefront-tracking location solver and a recently developed tomography model derived from active and passive source data. The relocated hypocenters are generally shallower and more concentrated beneath the crater compared to their catalog locations. The mean hypocenter movement from catalog locations is 2.86 km, with an averaged depth shift of 2.53 km upward. Comparison between 2017 hypocenters located using all of the available phase picks and those located using only the catalog picks from the permanent network suggests the improved hypocenters mostly resulted from the location solver and the 3D velocity model, with smaller changes due to the dense three-component array. Applying the same hypocenter estimation method to phase picks for all events from 1997 to 2004 and 2008–2021, we found a concentration of seismicity between sea level and ~ 1 km above it before and after the 2004–2008 eruption. The new results suggest that the seismogenic structure in the shallow magmatic system quickly re-equilibrated to its earlier state after the dome-building eruption.