Flood basalts appear to form during the initiation of hotspot magmatism. The Columbia River basalts (CRB) represent the largest volume of flood basalts associated with the Yellowstone hotspot, yet their source appears to be in the vicinity of the Wallowa Mountains, about 500 km north of the projected hotspot track. These mountains are composed of a large granitic pluton intruded into a region of oceanic lithosphere affinity. The elevation of the interface between Columbia River basalts and other geological formations indicates that mild pre-eruptive subsidence took place in the Wallowa Mountains, followed by syn-eruptive uplift of several hundred metres and a long-term uplift of about 2 km. The mapped surface uplift mimics regional topography, with the Wallowa Mountains in the centre of a 'bull's eye' pattern of valleys and low-elevation mountains. Here we present the seismic velocity structure of the mantle underlying this region and erosion-corrected elevation maps of lava flows, and show that an area of reduced mantle melt content coincides with the 200-km-wide topographic uplift. We conclude that convective downwelling and detachment of a compositionally dense plutonic root can explain the timing and magnitude of Columbia River basalt magmatism, as well as the surface uplift and existence of the observed melt-depleted mantle.