Abstract Inland waters emit and export large quantities of carbon (C), and the balance between emission and export determines the role of inland waters in the global C cycle. Modeling studies of stream‐lake networks suggest that C emission‐to‐export ratios (emission:export) are higher in lake‐rich networks with longer network residence times (NRT), yet empirical evidence supporting these patterns remains limited. We sampled 362 stream segments and 42 lakes across 32 nested arctic stream‐lake networks, repeated across four seasons with contrasting environmental conditions. The data show that lake‐rich networks have much longer NRT and higher C emission:export regardless of environmental conditions, while overall C emission:export increased during warmer low‐flow periods. Our findings stress the importance of accounting for lakes within stream networks and simultaneously quantifying multiple C fates when assessing the role of inland waters in the C cycle.