Although stream ecosystems are recognized as an important component of the global carbon cycle, the impacts of climate-induced hydrological extremes on carbon fluxes in stream networks remain unclear. Using continuous measurements of ecosystem metabolism, we report on the effects of changes in snowmelt hydrology during the anomalously warm winter 2013/2014 on gross primary production (GPP), ecosystem respiration (ER), and net ecosystem production (NEP) in an Alpine stream network. We estimated ecosystem metabolism across 12 study reaches of the 254 km² subalpine Ybbs River Network (YRN), Austria, for 18 months. During spring snowmelt, GPP peaked in 10 of our 12 study reaches, which appeared to be driven by PAR and catchment area. In contrast, the winter precipitation shift from snow to rain following the low-snow winter in 2013/2014 increased spring ER in upper elevation catchments, causing spring NEP to shift from autotrophy to heterotrophy. Our findings suggest that the YRN transitioned from a transient sink to a source of carbon dioxide (CO₂) in spring as snowmelt hydrology differed following the high-snow versus low-snow winter. This shift toward increased heterotrophy during spring snowmelt following a warm winter has potential consequences for annual ecosystem metabolism, as spring GPP contributed on average 33% to annual GPP fluxes compared to spring ER, which averaged 21% of annual ER fluxes. We propose that Alpine headwaters will emit more within-stream respiratory CO₂ to the atmosphere while providing less autochthonous organic energy to downstream ecosystems as the climate gets warmer.