The supply of organic carbon to large river systems is generally poorly understood. At issue are the relative contributions of in-channel, headwater catchment and flood plain primary production and how these contributions vary with flow conditions. Recent work has indicated that fine suspended particulate organic matter (FSPOM) is the most important form of carbon for riverine aquatic food webs. C/N and d13C ratios in samples of FSPOM collected from along a large lowland river system show that during a 1 in 10 year flood catchment soil sources dominate. During non-flood periods the contribution from soil organic matter and C3-riparian vegetation decreases systematically with distance downstream while carbon derived from in-channel primary production increases, dominating (>75%) in the lower reaches. The d13C ratios and radiocarbon dating indicates that the in-channel primary producers are using carbon derived from the breakdown of terrestrial organic matter photosynthesized from the atmosphere 40–50 years ago. These results show that organic matter derived from catchment soils is a major carbon source for large rivers, and reveals the importance of in-channel carbon cycling and primary production.