Abstract. Arctic warming is causing permafrost thaw and release of organic carbon (OC) to fluvial systems. Permafrost-derived OC can be transported downstream and degraded into greenhouse gases that may enhance climate warming. Susceptibility of OC to decomposition depends largely upon its source and composition, which vary throughout the seasonally distinct hydrograph. Most studies on carbon dynamics to date have focused on larger Arctic rivers, yet little is known about carbon cycling in lower-order rivers and streams. Here, we characterize the composition and sources of OC, focusing on less studied particulate OC (POC), in smaller waterways within the Kolyma River watershed. Additionally, we examine how watershed characteristics control carbon concentrations. In lower-order systems, we find rapid initiation of primary production in response to warm water temperatures during spring freshet, shown by decreasing δ13C-POC, in contrast to larger rivers. This results in CO2 uptake by primary producers and microbial degradation of mainly autochthonous OC. However, if terrestrially derived inorganic carbon is assimilated by primary producers, part of it is returned via CO2 emissions if the autochthonous OC pool is simultaneously degraded. As Arctic warming and hydrologic changes may increase OC transfer from smaller waterways to larger river networks, understanding carbon dynamics in smaller waterways is crucial.