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Abstract Resilience, measured by the distribution of passage times between alternate states, indicates persistence of a state in stochastic dynamic systems such as blooms of cyanobacteria in lakes. We used high‐frequency datasets to compare the resilience of low and high states of phycocyanin, a pigment indicator of cyanobacteria, in Lake Mendota, Wisconsin, USA, for three growing seasons that ranged sevenfold in external phosphorus (P) load. Each year we observed 139–265 passage times across the unstable threshold that separated the low‐ from high‐phycocyanin states. Each sample of passage times is highly skewed with low median, larger mean, much larger SD, and wide tails extending to long lifetimes of a state. About 25% of events, whether low or high phycocyanin, lasted a day or more. Among these 3 years of contrasting external P load, there were no discernible differences in the resilience of either ecosystem state. We attribute this lack of contrast to the sustained recycling of P from sediments and the high stochasticity of phycocyanin in this lake.