The south-central portion of the Columbia Basin in Washington State (USA), although not the primary eruptive center for the Columbia River Basalt (CRB), contains the thickest package of CRB lavas, at over 4 km. Prior to CRB deposition the region was a sediment-filled rift basin dating back to the early Eocene. Previous studies interpret a lower-crust, high-velocity body below the thick basalt deposits as a syn-extensional magmatic underplate. CRB layers thicken toward the center of the basin, revealing a pulse of subsidence during deposition that ceased coincident with cessation of CRB eruptions. We propose a subsidence mechanism based on metamorphic transition of the underplate from basalt to eclogite facies, driven by the increased pressure of CRB loading. We demonstrate the plausibility of our interpretation using numerical models of the mechanical and chemical components of the system. Further, we constrain the effective elastic thickness of the Miocene Columbia Basin lithosphere, finding it to be much thinner (5–10 km) than previous estimates.