The growing threat of abrupt and irreversible changes to the functioning of freshwater ecosystems compels robust measures of tipping point thresholds. To determine benthic cyanobacteria regime shifts in a potable water supply system in the tropical Andes, we conducted a whole ecosystem-scale experiment in which we systematically diverted 20 to 90% of streamflow and measured ecological responses. Benthic cyanobacteria greatly increased with a 60% flow reduction and this tipping point was related to water temperature and nitrate concentration increases, both known to boost algal productivity. We supplemented our experiment with a regional survey collecting > 1450 flow-benthic algal measurements at streams varying in water abstraction levels. We confirmed the tipping point flow value, albeit at a slightly lower threshold (40-50%). A global literature review broadly confirmed our results with a mean tipping point at 58% of flow reduction. Our study provides robust in situ demonstrations of regime shift thresholds in running waters with potentially strong implications for environmental flows management.