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High mountain lakes are increasingly recognized as sentinel ecosystems of global change. Monitoring phytoplankton changes or reconstructing their composition from sedimentary records can help identify systemic changes in these lakes and their catchments.This study aimed to evaluate the distribution of the major phytoplankton groups in high mountain lakes across environmental gradients and identify tipping points in relative dominance. The phytoplankton groups were estimated using pigment‐based chemotaxonomy in 79 lakes in the Pyrenees selected to cover the bedrock and elevation gradients. Fifty‐four environment variables were considered, including in‐lake and catchment descriptors.Redundancy analyses showed that in‐lake descriptors override the explicative capacity of landscape variables. Generalized additive models and multivariate regression trees showed that water hardness, trophic state and food‐web descriptors were, in this order, the most influential factors determining phytoplankton group dominance. Calcium concentration of about 200 μeq L−1 defined the threshold between soft waters—with chrysophytes and chlorophytes showing a higher affinity for them—and harder waters that favour diatoms and cyanobacteria. Across the trophic gradient, there was a threshold at ~5 μg L−1 of total phosphorus (TP), chrysophytes being dominant below that TP value and cryptophytes above. The dominance of chlorophytes and cryptophytes increased with the density of macrozooplankton. Chrysophytes were significantly lower and diatoms higher in lakes with fish.Synthesis. The relative abundance of phytoplankton groups in temperate high mountain lakes responds in a nonlinear way to the hardness of the water in the range 20–1195 Ca2+ μeq L−1 and the trophic state in the range 0.94–19 TP μg L −1. The thresholds across water hardness and trophic state gradients coincide with studies based on other organisms, pointing to a robust typology for mountain lakes that should be considered when selecting global change sentinel lakes and anticipating abrupt transitions across these thresholds. [ABSTRACT FROM AUTHOR]