High-mountain ecosystems are experiencing acute effects of climate change, most visibly through glacier recession and the ‘greening’ of the terrestrial environment. The streams draining these landscapes are affected by these shifts, integrating hydrologic, geologic, and biological signals across the watershed. We examined the organic and inorganic carbon dynamics of streams in four Alpine watersheds in Switzerland to assess how glacier loss and vegetation expansion are affecting the carbon cycle of these high mountain ecosystems. We find that organic carbon concentration and fluorescence properties associated with humic-like compounds increase with vegetation cover within a catchment, demonstrating the increasing importance of allochthonous carbon sources following glacier retreat. Meanwhile, streams transitioned from carbon dioxide sinks to sources with decreasing glacier coverage and increasing vegetation coverage, where the relative importance of chemical weathering and soil respiration likely determine the balance. Periods of sink behavior were also observed in non-glaciated streams, possibly indicating carbon dioxide uptake as a result of chemical weathering could be more common in high-mountain, minimally vegetated environments than previously known. Together, these results demonstrate the dramatic shift in carbon dynamics of alpine streams following glacier retreat, with significant changes to both the organic and inorganic carbon cycles. The clear link between the terrestrial and aquatic zones further emphasizes the coupled dynamics with which all hydrologic and biogeochemical changes in these ecosystems should be considered.