A paucity of research exists regarding the millennial-scale response of inland alluvial streams to abrupt base-level fall. Studies of modern systems indicate that, over short time scales, the response is a diffusion-like process of upstream-propagating incision. In contrast, evidence from the lower Chippewa River (LCR), located in the upper Midwest of the USA, suggests that autogenic controls operating over time scales of several millennia can overwhelm diffusion, resulting in incision that is prolonged and episodic. During the Last Glacial Maximum, the LCR drained the Chippewa Lobe of the Laurentide Ice Sheet to the glacial upper Mississippi River (UMR). As a meltwater stream, it aggraded and filled its valley with glacial outwash, as did its largest tributaries, which were also meltwater streams. Its nonglacial tributaries aggraded, too, filling their valleys with locally derived sediment. During deglaciation, the UMR incised at least twice, abruptly lowering the LCR's base level — ~15m at 16ka or earlier and an additional 40m at ca. 13.4ka. Each of these base-level falls initiated incision of the LCR, led by upstream migrating knickpoints. The propagation of incision has, however, been a lengthy process. The optically stimulated luminescence (OSL) ages of terrace alluvium indicate that, by 13.5ka, incision had advanced up the LCR only 15km, and by 9ka, only 55km. The process has also been episodic, resulting in the formation of fill-cut terraces (inferred from GPR surveys and exposures of terrace alluvium) that are younger and more numerous in the upstream direction. Autogenic increases in sediment load and autogenic bed armoring, the result of periodic tributary-stream rejuvenation and preferential winnowing of fines by the incising river, may have periodically caused knickpoint migration and incision to slow and possibly stop, allowing lateral erosion and floodplain formation to dominate. A decline in sediment flux from stabilizing incised tributary stream systems would have led to renewed knickpoint migration and incision when floods of sufficient magnitude to breach the channel armor occurred. Minimal floodplain development along the upper section of the present-day LCR, along with the channel morphology of an unstable wandering gravel-bed river immediately downstream from it, suggest that the river is still responding to the base-level falls that happened many millennia ago. The autogenic controls on the LCR's response to UMR incision are a direct consequence of the thick fills of noncohesive sediment that accumulated in its valley and the valleys of its tributary streams during the Late Wisconsinan, making the LCR a prime example of a former proglacial river that remains a paraglacial fluvial system. •The response of former proglacial alluvial streams to base-level fall can be complex.•Autogenic variations in sediment supply and bed armoring are likely key controls.•The result is upstream propagating incision that is episodic and prolonged.•Abundant glacial-age alluvial fill likely affects the autogenic incision process.•Former proglacial streams can be characterized as paraglacial fluvial systems.