For more than a century, researchers have debated the route of the Snake River across the northern Cordillera and U.S. Pacific Northwest, including the associated incision history of Hells Canyon. Here, we use detrital zircon U-Pb provenance analysis of Miocene strata upstream and downstream of Hells Canyon to constrain the evolution in fluvial pathways over time. Downstream of Hells Canyon, we show that the ca. 10−6 Ma Clarkston Heights gravel was dominantly sourced from the nearby Salmon and Clearwater rivers but also with substantial input from drainages that now flow into the western Snake River Plain. These same western Snake River Plain drainages were contributing to time-equivalent Lake Idaho strata, upstream of Hells Canyon, indicating a Hells Canyon fluvial connection between the western Snake River Plain and Columbia basin before 6 Ma. Results from Lake Idaho strata suggest a two-phased lacustrine history in the western Snake River Plain: Before ca. 6.0 Ma, lake strata were derived from local tributaries, suggesting that the western Snake River Plain was isolated from the modern upper Snake River system. Between ca. 4.3 Ma and 2.2 Ma, the source area expanded to include eastern tributaries in conjunction with migration of high-standing topography of the Yellowstone hotspot. Our results challenge the long-held hypothesis of “capture” of the Snake River through Hells Canyon. Instead, we infer that Hells Canyon was a long-established route for outflow of lakes occupying the western Snake River Plain, possibly intermittently, during a ca. 10−2 Ma phase of slow regional incision, followed by rapid incision in Hells Canyon starting ca. 2 Ma in conjunction with erosion of the topographic barrier impounding Lake Idaho.