Understanding the dynamics of the greater Yellowstone region requires constraints on deformation spanning million year to decadal timescales, but intermediate-scale (Quaternary) records of erosion and deformation are lacking. The Upper Snake River drainage crosses from the uplifting region that encompasses the Yellowstone Plateau into the subsiding Snake River Plain and provides an opportunity to investigate a transect across the trailing margin of the hotspot. Here, we present a new chronostratigraphy of fluvial terraces along the lower Hoback and Upper Snake Rivers and measure drainage characteristics through Alpine Canyon interpreted in the context of bedrock erodibility. We attempt to evaluate whether incision is driven by uplift of the Yellowstone system, subsidence of the Snake River Plain, or individual faults along the river's path. The Upper Snake River in our study area is incising at roughly 0.3 m/k.y. (300 m/m.y.), which is similar to estimates from drainages at the leading eastern margin of the Yellowstone system. The pattern of terrace incision, however, is not consistent with widely hypothesized headwater uplift from the hotspot but instead is consistent with downstream baselevel fall as well as localized deformation along normal faults. Both the Astoria and Hoback faults are documented as active in the late Quaternary, and an offset terrace indicates a slip rate of 0.25–0.5 m/k.y. (250–500 m/m.y.) for the Hoback fault. Although tributary channel steepness corresponds with bedrock strength, patterns of χ across divides support baselevel fall to the west. Subsidence of the Snake River Plain may be a source of this baselevel fall, but we suggest that the closer Grand Valley fault system could be more active than previously thought.