Spatio-temporal variability in fluvial incision rates in bedrock channels provides data regarding uplift and denudation histories of landscapes. The longitudinal profile of the Gunnison River (Colorado), tributary to the Colorado River, contains a prominent knickzone with 800 m of relief across it within the Black Canyon of the Gunnison. Average bedrock incision rates over the last 0.64 Ma surrounding the knickpoint vary from 150 m/Ma (downstream) to 400–550 m/Ma (within) to 90–95 m/Ma (upstream), suggesting it is a transient feature. Lava Creek B ash constrains strath terraces along a paleoprofile of the river. An isochron cosmogenic burial date in the paleo–Bostwick River of 870 ± 220 ka is consistent with the presence of 0.64 Ma Lava Creek B ash in locally derived, stratigraphically younger sediment. With 350 m of incision since deposition, we determine an incision rate of 400–550 m/Ma, reflecting incision through resistant basement rock at 2–3 times regional incision rates. Such contrast is attributed to a wave of transient incision, potentially initiated by downstream base-level fall during abandonment of Unaweep Canyon at ca. 1 Ma. Rate extrapolation indicates that the ∼700 m depth of Black Canyon has been eroded since 1.3–1.75 Ma. The Black Canyon knickpoint overlies a strong gradient between low-velocity mantle under the Colorado Rockies and higher-velocity mantle of the Colorado Plateau. We interpret recent reorganization and transient incision of both the Gunnison River and upper Colorado River systems to be a response to mantle-driven epeirogenic uplift of the southern Rockies in the last 10 Ma.