Stream geomorphic change is highly spatially variable but critical to landform evolution, human infrastructure, habitat, and watershed pollutant transport. However, measurements and process models of streambank erosion and floodplain deposition and resulting sediment fluxes are currently insufficient to predict these rates in all perennial streams over large regions. Here we measured long-term lateral streambank and vertical floodplain change and sediment fluxes using dendrogeomorphology in streams around the U.S. Mid-Atlantic, and then statistically modeled and extrapolated these rates to all 74 133 perennial, nontidal streams in the region using watershed- and reach-scale predictors. Measured long-term rates of streambank erosion and floodplain deposition were highly spatially variable across the landscape from the mountains to the coast. Random Forest regression identified that geomorphic change and resulting fluxes of sediment and nutrients, for both streambank and floodplain, were most influenced by urban and agricultural land use and the drainage area of the upstream watershed. Modeled rates for headwater streams were net erosional whereas downstream reaches were on average net depositional, leading to regional cumulative sediment loads from streambank erosion (−5.1 Tg yr−1) being nearly balanced by floodplain deposition (+5.3 Tg yr−1). Geomorphic changes in stream valleys had substantial influence on watershed sediment, phosphorus, carbon, and nitrogen budgets in comparison to existing predictions of upland erosion and delivery to streams and of downstream sediment loading. The unprecedented scale of these novel findings provides important insights into the balance of erosion and deposition in streams within disturbed landscapes and the importance of geomorphic change to stream water quality and carbon sequestration, and provides vital understanding for targeting management actions to restore watersheds.