The flow of organic matter (OM) along rivers and its retention within floodplains are fundamental to the function of aquatic and riparian ecosystems and are significant components of terrestrial carbon storage and budgets. Carbon storage and ecosystem processing of OM largely depends upon hydrogeomorphic characteristics of streams and valleys. To examine the role of channel complexity on carbon dynamics in mountain streams, we (1) quantify organic carbon (OC) storage in sediment and wood along 24 forested stream reaches in the Rocky Mountains of CO, U.S.A., (2) employ six years of logjam surveys and examine related morphological factors that regulate sediment and carbon storage, and (3) utilize fluorescence spectroscopy to examine how the composition of OM in surface water and floodplain soil leachates is influenced by valley and channel morphology. We find that lower-gradient stream reaches in unconfined valley segments at high elevations store more OC per area than higher-gradient reaches in more confined valleys, and those at lower elevations. We find that limited storage of fine sediment and increased mineralization of OC in multithread channel reaches decrease storage per area compared to simpler single-thread channel reaches. Results suggest that the positive feedbacks between channel complexity and persistent channel-spanning logjams that force multiple channels to flow across valley bottoms limit the aggradation of floodplain fine sediment, and promote hotspots for the transformation of OM. These multithread hotspots likely increase ecosystem productivity and ecosystem services by filtering dissolved organic carbon with potential to decrease contaminants associated with organic matter from surface water.