The range of environmental conditions in marine pelagic ecosystems is characterized by seasonality, particularly in mid and high latitudes. Annual cycles of light availability and water temperature are central to processes in pelagic food webs and drive the phenology of planktonic organisms. Using high resolution data of 24 phytoplankton species observed at Helgoland Roads (North Sea) during the period from 1962 to 2014, we analyzed the phenological response to long-term changes in the hydro-climatic conditions. We estimated timing by calculating the date of 50th percentile of cumulative abundance by taking into account both unimodal and bimodal (spring and autumn) peak structures. We show that species-specific preferences in combination with seasonally varying trends in environmental parameters led to a complex phenological response pattern. Species showing widely overlapping timing windows can exhibit different phenological responses. Both diatoms and dinoflagellates exhibit significant changes in seasonal peak timing (earlier/later), but some species show a remarkable constancy over the entire period. The intra-annual variability of timing strongly differs between different species, also due to basic differences in the environmental variability during the year. Shifts of the majority of species reflect long-term displacements in the occurrence of water temperature ranges within the year. On the long-term, only a few species show significant relationships between annual timing and peak abundance. Such complexity illustrates the uncertainty of making conclusions about potential future ecological development related to climate change.