Sediment deposition on floodplains is essential for the development and maintenance of riparian ecosystems. Upstream erosion is known to influence downstream floodplain construction, but linking these disparate processes is challenging, especially over large spatial and temporal scales. Sediment fingerprinting is thus a robust tool to establish process linkages between downstream floodplain development and sediment production in distal headwater basins. Here we use sediment geochemistry to connect historical erosion in several tributaries of the Yampa River in Colorado and Wyoming, USA, to the construction of downstream floodplains on which extensive cottonwood forests established. Using a combination of conventional techniques and the relatively novel machine-learning random forest algorithm, we build multiple fingerprints of diagnostic geochemical tracers that are then input into a Bayesian mixing model to apportion provenance of floodplain sediment. Sediment samples for provenance analysis were collected from an excavated floodplain in Deerlodge Park on the Yampa River at the rooting surface of the surrounding cottonwood forest and dominantly comprised of very fine (4Φ) sand. Fingerprinting analysis of the 4Φ fraction of collected floodplain sink (n = 38) and tributary source (n = 218) samples revealed floodplain sediment to be dominantly sourced from the tributaries of Muddy Creek (45 ± 4%) and Sand Wash (42 ± 6%). Dendrochronology results moreover indicate the Deerlodge floodplain sediment was deposited in ∼1912, which falls squarely within the time (1880–1940) these tributaries were actively eroding. Taken together, study results indicate a demonstrable link between historical tributary erosion and downstream floodplain construction and concomitant forest establishment. Our findings suggest processes operating in tributary watersheds play an important role in the dynamics of large rivers and emphasize both the need for holistic, collaborative management of sediment as an essential resource and the potential to utilize sediment fingerprinting to inform and direct river ecosystem management.