Loads and yields of dissolved and particulate nitrogen (N) and phosphorus (P) were measured and modeled at three locations on the Yukon River (YR) and on the Tanana and Porcupine Rivers in Alaska during 2001–2005. Total export of N and P upstream of Yukon Delta averaged 120 Gg N a−1 and 56 Gg P a−1, respectively, with 43.5% of total N (TN) as dissolved organic N, and 98% of total P (TP) as particulate phosphorus. Approximately half of the annual export of TN and TP occurred during spring. Hydrologic yields of TN (5.6–13.3 mmol N m−2 a−1) and TP (0.8–9.0 mmol P m−2 a−1) were least in the Porcupine basin and greatest in the Tanana basin and were proportional to water yield. Comparison of current and historical dissolved organic matter (DOM) export from the basin indicates decreased DON export with respect to total water discharge during summer and autumn in recent decades. Any possible climate-related change in annual water discharge will result in proportional changes in N and P export.