The cross-system exchange of energy and nutrients (subsidies) is a core attribute of landscapes that controls productivity and community dynamics in recipient systems. Such exchanges are likely to be disrupted by human influences. Inland waters receive significant subsidies from inflows from the surrounding landscape. Hydrologic modifications by water extraction, damming or altered precipitation patterns affect the magnitude and timing of flow extremes, which disrupts longitudinal, lateral and vertical connectivity in river networks. How subsidy transport responds to flow extremes has been little explored because watershed budgets usually do not consider the influence of floods. We measured the effects of storm-flows on organic carbon dynamics (concentration and standing stock) and projected how altered hydrologic variability might affect organic carbon accumulation and transport. We sampled dissolved and particulate organic carbon concentration at base- and storm-flow conditions in 19 stream sites over 2 years and modelled annual carbon fluxes. The highest flow events (5% of time) dominated the annual export of dissolved (39%) and fine particulate (59%) organic carbon. High flows increased the transport of particulate relative to dissolved organic carbon and reduced the accumulation of benthic coarse organic carbon. Minor changes to flow variability and storm-flow magnitude or frequency will strongly affect exchange among systems, with substantial consequences for ecosystem function. Shifts in the extremes of hydrological variability must be considered to ensure the longitudinal, lateral and vertical subsidy dynamics in freshwater systems.