Inland waters are major sources of CO2 to the atmosphere. The origin of this CO2 is often elusive, especially in high‐altitude streams that remain poorly studied at present. Here we study the spatial and seasonal variations in streamwater CO2, its potential sources and drivers in an Alpine stream network (Switzerland). High‐resolution sampling combined with stable isotope analysis and mixing models enabled us to capture the fine‐scale spatial heterogeneity in streamwater pCO2 as the stream network expanded and contracted during seasons. We identified soil respiration as a major source of CO2 to the stream. We also identified a major groundwater upwelling zone as an ecosystem ‘control point’ that disproportionately influenced stream biogeochemistry. This was particularly pronounced when the stream network expanded during snowmelt, when it covered a five times larger area compared to winter (35 300 m2 compared to 7 100 m2). Downstream from this ‘control point’, CO2 evaded rapidly owing to high gas transfer velocity. The stream network was a net source of CO2 to the atmosphere with an average areal evasion flux of 30.1 (18.0–43.1) μmol m‐2 s‐1 and a total flux at network scale ranging from 237 (141–339) kg C d‐1 in winter to 1793 (1069–2565) kg C d‐1 during spring snowmelt. Our study highlights the role of stream network dynamics and ‘control points’ for the CO2 dynamics in high‐altitude streams.