Understanding species phenology and temporal co-occurrence across trophic levels is essential to assess anthropogenic impacts on ecological interactions. We analyzed 15 yr of monitoring data to identify trends and drivers of timing and magnitude of bloom-forming phytoplankton and diverse zooplankton taxa in the central Baltic Sea. We show that the timings of phytoplankton blooms advance, whereas crustacean zooplankton seasonal timings remain constant. This increasing offset with the spring bloom is linked to the decline of Pseudocalanus, a key copepod sustaining pelagic fish production. The majority of copepod and cladoceran taxa, however, are co-occurring with summer blooms. We also find new developing fall blooms, fueling secondary production later in the season. Our study highlights that response to climate change differs within and between functional groups, stressing the importance of investigating plankton phenologies over the entire annual cycle in pelagic systems.