The decoupling of trophic interactions could be one of the severe consequences of climate warming in aquatic systems. The timing of phytoplankton blooms, in particular, can affect competition within the plankton community as well as food-web interactions with zooplankton and fish. Using long-term data from Helgoland Roads in the southern North Sea, we examine diatom seasonality, using three representative diatom species combined with environmental and copepod time series over the last four decades. The long-term annual abundances of Guinardia delicatula, Thalassionema nitzschioides and Odontella aurita exhibited interannual variations and dissimilar cyclic patterns during the time period under study (1962–2008). Of the three diatoms, G. delicatula showed a significant trend towards earlier bloom timings for 1962–2008 and a later decline of its abundance over time was found. Grazing and water transparency explained most of the bloom timing fluctuations of the diatoms considered. The annual timing of occurrences of each diatom species was correlated with their preceding concentrations. Earlier bloom timings occurred when autumn/winter concentrations were higher than average and later bloom timings occurred when autumn/winter concentrations were lower than average. Different environmental and predation variables related to the diatom bloom timings were found suggesting that climate warming might not affect the onset of the blooms of the three diatom species in the same manner. The results of the multiple linear regression analyses showed that the timings of decline of the three diatoms were mainly correlated with decreasing nutrient concentrations. Sunshine duration could prolong the duration of the blooms of T. nitzschioides and O. aurita provided that enough nutrients were available. In the case of G. delicatula, however, sunshine duration was negatively correlated with its end of the growth period. G. delicatula and T. nitzschioides showed later decreases in abundances under warmer spring and summer temperatures. Such species specific differences in the sensitivity to the forcing variables could lead to shifts in community structure and could ultimately have wider implications to the overall ecosystem health of the North Sea.