Published research emphasizes rapid downstream export of terrestrial carbon from mountainous headwater rivers, but little work focuses on mechanisms that create carbon storage along these rivers, or on the volume of carbon storage. Here we estimate organic carbon stored in diverse valley types of headwater rivers in Rocky Mountain National Park, CO, USA. We show that low-gradient, broad valley bottoms with old-growth forest or active beaver colonies store the great majority of above- and below-ground carbon. These laterally unconfined valley segments constitute <25% of total river length, but store ∼ 75% of the carbon. Floodplain sediment and coarse wood dominate carbon storage. Our estimates of riverine carbon storage represent a previously undocumented but important carbon sink. Our results indicate that: not all mountainous rivers rapidly export carbon; not all valley segments are equally important in carbon storage; and historical changes in riverine complexity have likely reduced carbon storage.

Biogeochemical processing of dissolved organic matter (DOM) in headwater rivers regulates aquatic food web dynamics, water quality, and carbon storage. Although headwater rivers are critical sources of energy to downstream ecosystems, underlying mechanisms structuring DOM composition and reactivity are not well quantified. By pairing mass spectrometry and fluorescence spectroscopy, here we show that hydrology and river geomorphology interactively shape molecular patterns in DOM composition. River segments with a single channel flowing across the valley bottom export DOM with a similar chemical profile through time. In contrast, segments with multiple channels of flow store large volumes of water during peak flows, which they release downstream throughout the summer. As flows subside, losses of lateral floodplain connectivity significantly increase the heterogeneity of DOM exported downstream. By linking geomorphologic landscape-scale processes with microbial metabolism, we show DOM heterogeneity increases as a function of fluvial complexity, with implications for ecosystem function and watershed management.