Annually recurring environmental processes such as the cycle of temperature and light drive the phenology of marine plankton populations. Improved knowledge about the homogeneity and amplitude of the phenological response of phytoplankton to climate change is essential for an assessment of ecological consequences on the marine ecosystem. We analyzed phenological variability of 21 phytoplankton species monitored work-daily at Helgoland Roads from 1962-2015. We used a function of “Weibull”-type to estimate phenological dates of species-specific abundance peaks. The combination of derived dates and peak abundances formed the basis for the analyses of long-term changes in phenological time slots and associated environmental conditions. Species-specific preferences in combination with seasonally varying environmental trends resulted in a complex pattern of phenological long-term response. Phenological trends showed both constant occurrence and shifts to an earlier or later occurrence. Co-occurring phytoplankton species were shown to exhibit different phenological trends even within identical time slots. Differences in species-specific trends in timing also reflected the seasonally varying shifts in water temperature ranges due to warming. In spring and summer, the main patterns of common variability in timing were associated with different abiotic and biotic drivers. The majority of species showed more narrow time slots related to the occurrence of higher peaks. Considering the variation of species occurrence in their “typical” time window provided insight in terms of assigning the effect of environmental drivers on inter-annual phenological variation. Phytoplankton species with similar long-term trends in timing (days) showed different trends in biomass, i.e. the phenological changes resulted from different ecological responses to environmental change. The local character of environmental trends at Helgoland underpins the limits for comparison of findings between different measuring sites or wider areas, such as the North Sea. The study emphasizes the benefit and necessity of a highly resolved phytoplankton record for a true understanding of long-term ecological changes in a highly dynamic marine environment such as the North Sea.