Carbon fixation and respiration in flowing waterways play significant roles in global and regional carbon budgets, yet how land use and watershed management interact with temporal disturbances (storms) to influence metabolism remains poorly understood. Here, we combine long-term with synoptic sampling of metabolism and its variable controls in neighboring watersheds of the Chesapeake Bay to resolve limiting factors and critical timescales associated with recovery from disturbance. We found that, relative to predictions of the river continuum concept, focal streams have "disrupted" carbon cycles, with carbon balances closer to zero, and, in some cases, tighter coupling between gross primary production (GPP) and ecosystem respiration (ER), attributable to carbon limitation. Carbon became limiting to ER where flashy storm hydrographs and simplified channel geomorphology inhibited accumulation of fine sediment. Shannon entropy analysis of timescales revealed that fine sediment served as a time-release capsule for nutrients and carbon over 4-6 months, fueling biogeochemical transformations. Loss of fines through hydraulic disturbance had up to 30-d impacts on GPP and 50-d impacts on ER in the stream with carbon limitation. In contrast, where GPP and ER were not tightly coupled, recovery occurred within 1 d. Results suggest that a complex interplay between nutrient and carbon limitation and mechanical and chemical disturbance governs patterns and consequences of disrupted carbon cycling in urban streams. Carbon limitation and tight GPP/ER coupling enhance the vulnerability of stream ecosystem functions, but best management practices that target stormflow reduction and channel geomorphic diversity can break that coupling and minimize carbon cycle disruptions.Flowing inland waters play an outsized role in global and regional carbon cycling, with sequestration and atmospheric exchange fluxes of the same order of magnitude as terrestrial and marine sequestration (Battin et al. 2008(Battin et al. , 2009Tranvik et al. 2009). It has been estimated that half of the carbon entering stream networks from terrestrial inputs is released to the atmosphere as CO 2 , less than half is transported to oceans, and the remaining fraction is buried (Cole et al. 2007;Raymond et al. 2013). Stream metabolism itself composes 28% of all CO 2 emissions from streams in the U.S. . This mineralization of terrestrial organic material and respiratory denitrification within stream networks lessen carbon and nutrient exports to downstream estuaries and the incidence of harmful algal blooms and eutrophication (Alexander et al. 2007;Freeman et al. 2007;Alexander et al. 2009). Still, estimates of carbon cycling in inland waters remain poorly constrained (Regnier et al. 2013;Butman et al. 2016).Improved dissolved oxygen sensor technology (Almeida et al. 2014), combined with advances in stream metabolism modeling (Holtgrieve et al. 2010;Demars and Manson 2013;Holtgrieve et al. 2015), have made it possible to generate long-term metabolism records fo...