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Abstract Terrestrial plants are sensitive indicators of global warming because their annual cycles of growth and senescence are changing as warming proceeds. Single celled algae are distinct life forms capable of population bursts in any season, so there is uncertainty about phytoplankton phenology as a comparable indicator of global warming. We analyzed 4+ decades of monthly chlorophyllameasurements at two sites in San Francisco Bay and found abrupt shifts during summer months leading to a 48‐day advance in the annual pattern of chlorophyll‐a accumulation at one site and a 36‐day delay at the other. These large phenological changes were not associated with changing temperature, but they were associated with changes in top–down control by bivalve filter feeders as biological communities were restructured by (1) introduction of a non‐native clam, and (2) a shift in atmospheric forcing of the NE Pacific. This study illustrates that changes in phytoplankton phenology are not necessarily responses to or indicators of global warming. However, they can be indicators of human disturbances and natural climate oscillations having effects large enough to mask the effect of climate warming.