Carbon and total suspended sediment (TSS) loads were investigated from April 2006 to March 2008 in the mountainous watershed of the Isère River, French Alps (5570 km2). The river bed has been highly impounded for hydroelectricity production during the last century. Hydraulic flushes are managed every year to prevent TSS storage within upstream dams. The Isère River has been instrumented for high-frequency monitoring of water, TSS by turbidity and carbon (organic, inorganic, dissolved and particulate) in order to evaluate the impact of natural floods and hydraulic flushes on annual loads. Annual TSS load which was estimated between 1.3 and 2.3 MT y−1 (i.e. 233 to 413 T km−2 y−1) highlighted the high erodibility of the Isère watershed. Annual carbon load was estimated between 173 103 T y−1 and 199 103 T y−1 (i.e 31 to 36 T km−2 y−1). About 80% of the annual carbon loads were inorganic. The impact of hydraulic flushes on annual loads appeared limited (less than 3% for annual TSS load and about 1.5% for annual carbon load), whereas the most important natural flood event contributed to 20% of the annual TSS load and 10% of the annual carbon load. Copyright © 2012 John Wiley & Sons, Ltd.