The Yukon River basin is a vast and diverse ecosystem covering more than 330,000 square miles, an area larger than Texas. Approximately 126,000 people live within the basin and depend on the Yukon River and its tributaries for drinking water, commerce, and recreational and subsistence fish and game resources.

Much of the Yukon River basin is underlain by permafrost containing vast amounts of organic carbon and nutrients. Recent climatic warming of the basin has resulted in lengthening of the growing season, melting of permafrost, deepening of the soil active layer, drying of upland soils, and shrinking of wetlands. These mostly terrestrial effects also affect the hydrology of the basin, changing the timing, magnitude, and fate of water and dissolved and particulate materials delivery to the Yukon River and its tributaries.

As permafrost melts, stored carbon and nutrients are expected to become available for decomposition by soil organisms or for export downstream and to the Bering Sea. Such changes can have numerous, far-reaching effects on the ecosystem, including increased emission of greenhouse gases such as carbon dioxide and methane; changes in stream productivity, including salmon populations; changes in the productivity and chemistry of the Bering Sea; and increased fire frequency. One important question is whether organic carbon export to rivers will increase or decrease downstream from large wetland areas presently having substantial carbon storage, such as Yukon Flats.

Because very few historical water-quality data are available for the Yukon River basin, scientists are unable to quantitatively assess potential effects of climate warming on aquatic ecosystems in the basin. In order to address these concerns, the U.S. Geological Survey conducted a comprehensive baseline water-quality characterization of the Yukon River and its major tributaries during 2000-05. The study included frequent water-quality sampling at a fixed-site network. In addition to the fixed-site sampling, intensive synoptic sampling of tributaries draining directly into the Yukon River was conducted along its entire length. This report contains observations of water and sediment quality made in the Yukon River basin during the synoptic sampling cruises in years 2002 and 2003. Chemical and biological data are presented for the Yukon River and its major tributaries between the towns of Eagle and St. Marys, Alaska.