To understand the variations of organic carbon inputs in high latitude rivers, we tracked the changes in fatty acid concentrations and their stable carbon isotopic compositions in dissolved (DOM, < 1 kDa), colloidal (COM, 1 kDa to 0.45 mu m) and particulate (POM, > 0.45 mu m) organic matter collected from the upper Yukon River (Alaska, USA) during ice-open season from May to September 2002. In spite of the high variability in discharge, total organic carbon in the river continuously declined from the beginning of snowmelt, while fatty acid contents (normalized to organic carbon in each pool) varied independently in the three organic pools with the largest fraction of total fatty acids in the POM. Fatty acid compositions in each pool were similarly dominated by short-chain saturated (14:0, 16:0, and 18:0) and monounsaturated [16:1 and 18: 1(n-9)] fatty acids (70-80%), while bacterial fatty acids [normal and branched 15:0 and 17:0 plus 18:1(n - 7)] comprised an important fraction (16-30% of the total) in all samples. The concentrations of individual fatty acids in the three pools varied greatly during the ice-open season, but the compound-specific stable carbon isotopic ratios of fatty acids in POM were less variable compared to those in DOM and COM. Mass balance calculation showed that land-derived fatty acids dominated in May (snowmelt) while aquatic produced fatty acids peaked in July, consistent with the maximum Chl-a concentration. In addition, bacteria-specific fatty acids (e.g., iso-15:0) had similar delta(13)C ratios in all three pools, with little difference from those of bulk carbon. Our results suggest that relative inputs of organic matter from various sources into the upper Yukon River are significantly affected by snowmelt, rainfall, soil erosion, discharge, aquatic production, and biochemical degradation. (c) 2006 Elsevier Ltd. All rights reserved.