Water samples were collected from the Yukon River near the Stevens Village Station from May to September 2002 and analyzed for nutrients (N, P, and Si) in dissolved, particulate, organic, and inorganic forms to examine temporal variations in nutrient concentrations, fluxes, and phase partitioning. Both NO3 and PO4 concentrations in the Yukon River were much lower than those of world rivers, with an average concentration of 2.43 ± 0.63 μM-N and 0.053 ± 0.040 μM-P, respectively. Si(OH)4 concentrations were more comparable to those of world rivers, with an average concentration of 82 ± 21 μM-Si. Integrated annual fluxes were 2.4 × 108 mole-NO3, 3.4 × 106 mole-PO4, and 8.7 × 109 mole-Si(OH)4, respectively. Nutrient discharge during the river ice open season contributed 73 to 95% of the annual flux depending on nutrient species. Within the total N pool transported by the Yukon River, dissolved inorganic N comprised 7 ± 4% and particulate N made up 25 ± 10%, while dissolved organic N (DON) was the dominant N species (with an average of 67 ± 10%). In contrast, P was predominantly partitioned in the particulate phase (with an average of 94 ± 6%), leaving 4 ± 5% of the total P in the dissolved organic phase and ∼2 ± 1% in the dissolved inorganic phase. The partitioning of N and P indicates that the transformation between dissolved and particulate or inorganic and organic phases may play a critical role in controlling the flux of bioavailable nutrients and thus the nutrient dynamics in the Yukon River Basin and its coastal region. Nutrient specific fluxes normalized to drainage area in the Yukon River Basin were 0.57 mmole/m2/yr for NO3, 0.012 mmole/m2/yr for PO4, and ∼19 mmole/m2/yr for Si(OH)4, respectively. The relatively low specific fluxes of NO3 and PO4 in the Yukon River Basin reflect its pristine status or little anthropogenic influence, whereas cold climate in the Arctic/subarctic region may be responsible for its lower Si(OH)4 specific flux, in agreement with a general trend of increasing Si specific flux with decreasing latitude in global river systems. A warming climate and thus deeper permafrost active layer in the Yukon River watershed would likely enhance the export flux of nutrients into the Bering Sea.