Forms and quantities of organic carbon (C) fluxes at the soil surface, and organic C exports from four small (1–2 ha) headwater catchments were quantified and contrasted in the seasonally dry southern Amazon for 1 year to compare C fluxes within the terrestrial ecosystem with exports to the aquatic ecosystem. At the soil surface, the flux of litterfall C was 43 times greater than the dissolved organic carbon (DOC) flux in throughfall, with the highest rates of C deposition during the dry season. The form and timing of organic C was reversed for watershed exports, where DOC comprised 59% of the annual total organic C export, and exports were greatest during the 4-month rainy season (63% of total annual exports). Fine particulate organic carbon (FPOC) in streamwater was a substantially larger flux than coarse particulate organic carbon (CPOC), representing 37 and 4% of total annual organic C exports, respectively. Particulate organic C exports exhibited substantial seasonal variability, with FPOC and CPOC mobilized primarily in the rainy season and strongly connected to storm events. Storm flow comprised 6% of total streamflow for the year studied, and 10% of streamflow during the rainy season. In the rainy season, over 90% of FPOC exports were transported by storm flow, while only 32% of DOC exports were exported by storm flow during this period. Streamwater DOC concentrations were found to increase linearly with increasing terrestrial litterfall during the dry season (r2 = 0·92, p < 0·001), indicating that in-stream processing of allochthonous litterfall is an important source of DOC during the dry season. Copyright © 2006 John Wiley & Sons, Ltd.