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Abstract Resilience was compared for alternate states of phytoplankton pigment concentration in two multiyear whole‐lake experiments designed to shift the manipulated ecosystem between alternate states. Mean exit time, the average time between threshold crossings, was calculated from automated measurements every 5 min during summer stratification. Alternate states were clearly identified, and equilibria showed narrow variation in bootstrap analysis of uncertainty. Mean exit times ranged from 13 to 290 h. In the reference ecosystem, Paul Lake, mean exit time of the low‐pigment state was about 100 h longer than mean exit time of the high‐pigment state. In the manipulated ecosystem, Peter Lake, mean exit time of the high‐pigment state exceeded that of the low‐pigment state by 30 h in the cascade experiment. In the enrichment experiment mean exit time of the low‐pigment state was longer than that of the high‐pigment state by about 100 h. Mean exit time is a useful measure of resilience for stochastic ecosystems where high‐frequency measurements are made by consistent methods over the full range of ecosystem states.