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Abstract Increases to summer Arctic rainfall and tundra thermal degradation are altering hydrological cycling in coastal watersheds with implications for carbon (C) cycling and transport of C to the atmosphere and coast. Arctic riverine research has focused on large rivers; however, small streams contribute significantly to vertical and longitudinal carbon dioxide (CO₂) fluxes. Despite the well‐established connection between hydrology and biogeochemistry, the impact of extreme rainfall events on Arctic aquatic C cycling remains a knowledge gap. This study characterized how hydrology, biogeochemistry, and geomorphology control the supply of CO₂to low order streams and their propensity to act as atmospheric CO₂sources. We characterize biogeochemical and hydrologic processes in unique reaches from a beaded stream and stream impacted by thermal erosion. Rainfall and its resulting increases to terrestrial‐aquatic connectivity drove the movement of CO₂and biodegradable dissolved organic C (BDOC) from soils into streams, however, BDOC mineralization only contributed a small portion of surface CO₂fluxes. Rain events likely stimulated stream benthic respiration, which led to CO₂contributions from net ecosystem production often exceeding surface CO₂fluxes and downstream CO₂transport. In addition, thermal degradation played a role in terrestrial‐aquatic connectivity of the streams. The erosion‐affected stream had inconsistent and smaller inputs of CO₂, had weaker heterotrophic conditions, and smaller CO₂emissions. Understanding how hydrologic regime, influenced by late summer rain events and stream morphology, controls the transport of CO₂and metabolism in small tundra streams will help improve predictions of landscape scale CO₂emissions from these critically understudied systems.