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ABSTRACT Marine heatwaves (MHWs) caused by multiple phenomena with days to months duration are increasingly common disturbances in ocean ecosystems. We investigated the impacts of MHWs on pelagic communities using spatially resolved time‐series of multiple trophic levels from the Southern California Current Ecosystem. Indices of phytoplankton biomass mostly declined during MHWs because of reduced nutrient supply (exceptingProchlorococcus) and were generally more sensitive to marine heatwave intensity than duration. By contrast, mesozooplankton (as estimated by zooplankton displacement volume) were somewhat more strongly correlated with MHW duration than intensity. Zooplankton anomalies were also positively correlated with fucoxanthin (diatom) anomalies, highlighting possible bottom‐up influences during MHWs. Mobile consumers (forage fish) showed more complex responses, with fish egg abundance declining during MHWs but not correlating with any MHW characteristics. Our findings provide partial evidence of how MHW characteristics can shape variable ecological responses due to the differing life spans and behaviours of different trophic levels.