The Nelson River, a subarctic river in north-central Manitoba, is the largest river discharging to Hudson Bay and its watershed has seen extensive land-modification in the upper reaches, permafrost thaw in the lower reaches, and hydroelectric development throughout. To characterize sources of sediment and particulate organic matter (OM) in the Nelson River system, and to identify processes influencing its transport to Hudson Bay, water quality parameters, Compound-Specific Stable Isotope (CSSI) fingerprinting, and Bayesian unmixing models were employed on terrestrial and instream samples. Distinct regional, longitudinal, and temporal differences in water quality parameters and particulate OM sources were observed among all three regions of the Nelson River system (upper Nelson River, Rat-Burntwood River, lower Nelson River). The application of CSSI fingerprinting and unmixing models showed that the dominant sources of OM to suspended sediment in the lower reaches of the Nelson River are proximally derived and comprise soils, upstream suspended sediment, river bed sediment, and tributary suspended sediment.