Riverine dissolved organic carbon (DOC) is a critical biogeochemical component that transmits information from Arctic soils to the Arctic Ocean, significantly influencing carbon dynamics in this unique ecosystem. As DOC travels downstream, it undergoes transformations that alter its composition and fate. The Yukon River serves as an effective testbed for modeling these dynamics, offering sufficient scale to capture key biogeochemical processes, simpler hydrology than other major Arctic rivers, and access to long-term DOC data for model validation. To investigate DOC transformations during transit, we adapted our Arctic Riverine Organic Macromolecular Model by applying regional-specific parameterizations. Our model simulates the transport and transformation of 15 organic macromolecules, including CDOM (Coloured Dissolved Organic Matter), proteins, polysaccharides, lipids, lignin phenols, and humic substances. Initial DOC concentrations were derived from surrounding observed soil organic carbon stocks, while chemical transformations and hydrological dynamics were modeled along the river’s course. Sensitivity and uncertainty analyses were conducted using a Monte Carlo approach under two experimental setups. Results revealed that variability in DOC and CDOM concentrations at the river mouth were predominantly driven by initial DOC concentration (~70% of variability explained) and dilution at confluence points (~10%). The refractory fraction of DOC explained 21-88% of the variability in 14 macromolecular concentrations. River velocity, which determines residence time, explained 8-47% of the variability in protein, polysaccharide, lipid, pigments, and lignin phenols at the river mouth. In contrast, chemical turnover times contributed only 1–5% to output variability. Our findings underscore the need for improved land-specific headwater observations, including seasonal soil moisture and lateral transport dynamics that control the initial tributary-specific DOC inputs. With accelerated permafrost thaw and increasing river discharge, extending our model to other Arctic River systems and seasons will enhance understanding of Arctic riverine carbon fluxes and their contributions to the Arctic Ocean.