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Abstract Purpose The equilibrium sediment exchange process is defined as instantaneous deposition of suspended sediment to the streambed countered by equal erosion of sediment from the streambed. Equilibrium exchange has rarely been included in sediment transport studies but is needed when the sediment continuum is used to investigate the earth’s critical zone. Materials and methods Numericalmodeling in the watershed uplands and streamcorridor simulates sediment yield and sediment source partitioning for the Upper South Elkhorn watershed in Kentucky, USA.We simulate equilibrium exchange when uplandderived sediment simultaneously deposits to the streambed while streambed sediments erode. Sediment fingerprinting with stable carbon isotopes allowed constraint of the process in a gently rolling watershed. Results and discussion Carbon isotopes work well to partition upland sediment versus streambed sediment because sediment deposited in the streambed accrues a unique autotrophic, i.e., algal, fingerprint. Stable nitrogen isotopes do not work well to partition the sources in this study because the nitrogen isotope fingerprint of algae falls in the middle of the nitrogen isotope fingerprint of upland sediment. The source of sediment depends on flow intensity for the gently rolling watershed. Streambed sediments dominate the fluvial load for low and moderate events, while upland sediments become increasingly important during high flows and extreme events.We used sediment fingerprinting results to calibrate the equilibrium sediment exchange rate in the watershed sediment transport model. Conclusions Our sediment fingerprinting and modeling evidence suggest equilibrium sediment exchange is a substantial process occurring in the system studied. The process does not change the sediment load or streambed sediment storage but does impact the quality of sediment residing in the streambed. Therefore, we suggest equilibrium sediment exchange should be considered when the sediment continuumis used to investigate the critical zone.We conclude the paper by outlining future research priorities for coupling sediment fingerprinting with watershed modeling.